R. Toby Pennington's research while affiliated with University of Exeter and other places

Publications (364)

Chapter
Cryptic species are organisms which look identical, but which represent distinct evolutionary lineages. They are an emerging trend in organismal biology across all groups, from flatworms, insects, amphibians, primates, to vascular plants. This book critically evaluates the phenomenon of cryptic species and demonstrates how they can play a valuable...
Article
Ziziphus (Rhamnaceae) is a widely distributed genus across the Australasian and African tropics with unusual diversity in habit, and many species of significance to people. Here, we quantify the environmental limits of Ziziphus species and examine inter‐specific relationships among functional traits, environment, biome, and range size. We developed...
Preprint
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Early natural historians - Compte de Buffon, von Humboldt and De Candolle - established ecology and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and...
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The shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiver-sity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxo-nomic impediment to biodiversity research and conservation planning. The taxonomic impedi...
Article
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The Brazilian Caatinga is considered the richest nucleus of the Seasonally Dry Tropical Forests (SDTF) in the Neotropics, also exhibiting high levels of endemism, but the timing of origin and the evolutionary causes of its plant diversification are still poorly understood. In this study, we integrate comprehensive sampled dated molecular phylogenie...
Article
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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
The shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiver-sity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxo-nomic impediment to biodiversity research and conservation planning. The taxonomic impedi...
Article
Full-text available
While we have largely improved our understanding on what biomes are and their utility in global change ecology, conservation planning, and evolutionary biology is clear, there is no consensus on how biomes should be delimited or mapped. Existing methods emphasize different aspects of biomes, with different strengths and limitations. We introduce a...
Preprint
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Plants are widely recognized as chemical factories, with each species producing dozens to hundreds of unique secondary metabolites. These compounds shape the interactions between plants and their natural enemies. Here we explore how plants generate chemical diversity, and what evolutionary processes have led to novel compounds and unique chemical p...
Data
Supporting Information 1. A list of all reviewed hybridisation studies based in the Neotropics.
Article
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Hybridisation can facilitate both evolutionary diversification and extinction and has had a critical role in plant evolution, with~ 25% of species known to hybridise in some temperate floras. However, in the species-rich neotropical flora, hybridisation’s role in the evolution of diversity remains unclear. Our review examines studies of hybridisati...
Article
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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...
Article
We introduce the concept of Biome Awareness Disparity (BAD)-defined as a failure to appreciate the significance of all biomes in conservation and restoration policy-and quantify disparities in (i) attention and interest, (ii) action, and (iii) knowledge amongst biomes in tropical restoration science, practice, and policy. By analysing 50,000 tweet...
Article
The papilionoid legume genus Ormosia (Fabaceae) comprises about 150 species of trees and exhibits a striking disjunct geographical distribution between the New World- and Asian and Australasian wet tropics and subtropics. Modern classifications of Ormosia are not grounded on a well-substantiated phylogenetic hypothesis and have been limited to just...
Article
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This special issue focuses on long‐term ecological monitoring in the tropics, with a particular focus, appropriate to Plants, People, Planet, on what it can offer both to local people and decision makers in tropical countries. Two of the contributed papers emphasise the role that long‐term, permanent monitoring plots can play in bringing together r...
Article
Tropical forests are the most diverse and productive ecosystems on Earth. While better understanding of these forests is critical for our collective future, until quite recently efforts to measure and monitor them have been largely disconnected. Networking is essential to discover the answers to questions that transcend borders and the horizons of...
Article
Understanding how species diversify and evolve in species-rich areas like the lowland rain forest in the Neotropics is critical for conservation in times of unprecedented threats. To determine how the Andean uplift, the formation of the Panama land bridge, and Pleistocene climatic fluctuations affected dispersal and diversification in the Sapotacea...
Article
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The Amazon forest is far from uniform, containing different forest types and even savannas, but quantitative analyses of this variation are lacking. Here, we applied ordination analyses to test the floristic differentiation among Amazonian vegetation types using data for virtually all known tree species occurring in the Amazon (8224), distributed a...
Article
1. The outstanding diversity of Amazonian forests is predicted to be the result of several processes. While tree lineages have dispersed repeatedly across the Amazon, interactions between plants and insects may be the principal mechanism structuring the communities at local scales. 2. Using metabolomic and phylogenetic approaches, we investigated t...
Book
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The urge to organise the world around us is an essential part of human nature. Naming and categorising enable us to store and access information ef ciently. The need to name and categorise extends to the natural world and, in particular, to living organisms. The science underpinning this area of knowledge is called Taxonomy, and is as old as humani...
Article
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This study investigated the current Leguminosae tree species composition in coastal forests over lithosoil soil or sandy plains in the eastern and central portion of Rio de Janeiro state, Brazil. A comparative study between the Atlantic Forest areas of the Southeast Region of Brazil was conducted to evaluate the influence of environmental variables...
Article
Full-text available
Global patterns of species and evolutionary diversity in plants are primarily determined by a temperature gradient, but precipitation gradients may be more important within the tropics, where plant species richness is positively associated with the amount of rainfall. The impact of precipitation on the distribution of evolutionary diversity, howeve...
Article
Full-text available
Premise: Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the "tree of life" are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have s...
Article
Aim. In savannas, a grass dominated ground layer is key to ecosystem function via grass-fire feedbacks that maintain open ecosystems. With woody encroachment, tree density increases, thereby decreasing light in the ground layer and potentially altering ecosystem function. We investigated how light availability can filter individual grass species di...
Article
Tropical biomes are the most diverse plant communities on Earth, and quantifying this diversity at large spatial scales is vital for many purposes. As macroecological approaches proliferate, the taxonomic uncertainties in species occurrence data are easily neglected and can lead to spurious findings in downstream analyses. Here, we argue that techn...
Article
Full-text available
Hybridisation has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing inter‐specific gene flow. However, hybridisation in Amazonia’s megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species,...
Article
Full-text available
Aim Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and...
Article
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The covid-19 pandemic led to rapid and large-scale government intervention in economies and societies. A common policy response to covid-19 outbreaks has been the lockdown or quarantine. Designed to slow the spread of the disease, lockdowns have unintended consequences for the environment. This article examines the impact of Colombia’s lockdown on...
Article
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Understanding of tropical forests has been revolutionised by monitoring in permanent plots. Data from global plot networks have transformed our knowledge of forests’ diversity, function, contribution to global biogeochemical cycles, and sensitivity to climate change. Monitoring has thus far been concentrated in rain forests. Despite increasing appr...
Article
Full-text available
Understanding of tropical forests has been revolutionized by monitoring in permanent plots. Data from global plot networks have transformed our knowledge of forests’ diversity, function, contribution to global biogeochemical cycles, and sensitivity to climate change. Monitoring has thus far been concentrated in rain forests. Despite increasing appr...
Preprint
Full-text available
The Neotropics is the most species-rich area in the world and the mechanisms that generated and maintain its biodiversity are still debated. This paper contributes to the debate by investigating the evolutionary and biogeographic history of the genus Ceiba Mill. (Malvaceae: Bombacoideae). Ceiba comprises 18 mostly neotropical species endemic to two...
Article
Full-text available
Aim: To test whether species distribution models (SDMs) can reproduce major macroecological patterns in a species-rich, tropical region and provide recommendations for using SDMs in areas with sparse biotic inventory data. Location: Northeast Brazil, including Minas Gerais. Time period: Present. Major taxa studied: Flowering plants. Methods: Specie...
Article
Full-text available
Aim: Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) an...
Article
Full-text available
The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KP...
Article
Full-text available
The historical course of evolutionary diversification shapes the current distribution of biodiversity, but the main forces constraining diversification are still a subject of debate. We unveil the evolutionary structure of tree species assemblages across the Americas to assess whether an inability to move or an inability to evolve is the predominan...
Article
Full-text available
The Cerrado is a biodiversity hotspot in central Brazil that is the largest expanse of savanna in the Neotropics. Here, we aim to identify and delimit biogeographic districts within the Cerrado, to provide a geographic framework for conservation planning and scientific research prioritization. We used data from 588 sites with tree species inventori...
Preprint
Full-text available
This pre-print is currently under consideration at Molecular Ecology. Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of species undergoing inter-specific gene flow. However, hybridization in Amazonia’s megadiverse tree flora was assumed to be extremely...
Article
Full-text available
Aim To quantify evolutionary transitions between tropical evergreen rain forest and seasonally dry biomes, to test whether biome transitions affect lineage diversification and to examine the robustness of these results to methodological choices. Location The tropics. Time period The Cenozoic. Major taxa studied The plant subfamily Bombacoideae (...
Article
Full-text available
Global patterns of species and evolutionary diversity in plants are primarily determined by a temperature gradient, but precipitation gradients may be more important within the tropics, where plant species richness is positively associated with the amount of rainfall. The impact of precipitation on the distribution of evolutionary diversity, howeve...
Data
List of angiosperm clades (nodes) used to date the phylogeny via fossil-derived calibrations, taxa assigned as a reference for fossil placement, minimum age used as offset, mean age of the clades, and their respective sources. Ages in myrs.
Data
List of 2,025 tree community surveys used in this study with their respective metadata, including sources, genus and species richness, lineage diversity (standardised effect size of phylogenetic diversity), climatic variables, protection status, and loss of native area over the last 30 years in the municipality where these communities occur.
Data
List of 1,100 angiosperm genera used in the phylogenetic reconstructions, their respective sources of rbcL and matK sequences, GenBank accession numbers, when applicable; collectors, collector numbers and herbaria where vouchers were deposited, when applicable. RBG = Royal Botanic Garden Edinburgh. Asterisk indicates the 852 genera used in the comm...
Article
Full-text available
Higher levels of taxonomic and evolutionary diversity are expected to maximize ecosystem function, yet their relative importance in driving variation in ecosystem function at large scales in diverse forests is unknown. Using 90 inventory plots across intact, lowland, terra firme, Amazonian forests and a new phylogeny including 526 angiosperm genera...
Article
Full-text available
Higher levels of taxonomic and evolutionary diversity are expected to maximize ecosystem function, yet their relative importance in driving variation in ecosystem function at large scales in diverse forests is unknown. Using 90 inventory plots across intact, lowland, terra firme, Amazonian forests and a new phylogeny including 526 angiosperm genera...
Article
Early botanical explorers invoked biogeographic history to explain the remarkable tree diversity of Neotropical forests. In this context, we review the history of Neotropical tree diversity over the past 100 million years, focusing on biomes with significant tree diversity. We evaluate hypotheses for rain forest origins, intercontinental disjunctio...
Article
Full-text available
Phylogenomics is increasingly used to infer deep‐branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep‐branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm famil...
Article
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Bastin et al .’s estimate (Reports, 5 July 2019, p. 76) that tree planting for climate change mitigation could sequester 205 gigatonnes of carbon is approximately five times too large. Their analysis inflated soil organic carbon gains, failed to safeguard against warming from trees at high latitudes and elevations, and considered afforestation of s...
Article
Full-text available
Various historical processes have been put forth as drivers of patterns in the spatial distribution of Amazonian trees and their population genetic variation. We tested whether five widespread tree species show congruent phylogeographic breaks and similar patterns of demographic expansion, which could be related to proposed Pleistocene refugia or t...
Article
Full-text available
Plant secondary metabolites are a key defence against herbivores, and their evolutionary origin is likely from primary metabolites. Yet for this to occur, an intermediate step of overexpression of primary metabolites would need to confer some advantage to the plant. Here we examine the evolution of overexpression of the essential amino acid, L‐tyro...
Article
Ecology, geography, morphology, and a combined phylogenetic analysis of DNA sequence variation support the recognition of the new species Luetzelburgia jacana (Leguminosae, Papilionoideae, vataireoid clade). This species is found in the inter-Andean Rio Cauca Valley in Colombia. Phylogenetic analyses of nine plastid and nuclear DNA sequences from 4...
Data
Sawfly MOTU accumulation curves when sampling over Inga host plant taxa, and when sampling over individuals. For each curve, the mean estimate is shown as a dark blue line and the standard deviation as a pale blue shaded region either side. The total numbers of Inga taxa and sawfly specimens in these analyses were 34 and 1286, respectively.
Data
MrBayes majority-rule consensus tree for the nuclear locus ITS2, sequenced for exemplars of each of the selected 41 jMOTU 1.5% COI MOTUs. Numbers above nodes indicate posterior probabilities. Taxon labels are colored to indicate membership of different MOTUs.
Data
MrBayes majority-rule consensus tree for the nuclear locus wingless, sequenced for exemplars of each of the selected 41 jMOTU 1.5% COI MOTUs. Numbers above nodes indicate posterior probabilities. Taxon labels are colored to indicate membership of different MOTUs.
Data
Molecular methods for PCR amplification of sawfly sequences.
Data
List of compounds putatively identified through matches to reference MSMS spectra on the Global Natural Products Social Molecular Networking database (https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp). The cosine score is a measure of the similarity of MS/MS-derived fragments between two compounds.
Data
MrBayes majority-rule consensus tree for the mitochondrial COI DNA barcode fragment. Numbers above nodes indicate posterior probabilities. Taxon label colors indicate membership of 1.5% sequence divergence jMOTU taxa, indicated by the labels at right.
Data
Metadata for all sawfly specimens collected in this study, including host plant and collection location, MOTU allocation (1.5% jMOTU taxa), and Genbank accession numbers for all sequenced gene fragments. Note that in our sampling system, each study site has independent collection numbers. Thus, it is possible for two Inga plants to have the same ho...
Data
Information on the ten sequence loci used for construction of the Inga species tree. Locus number, reference transcript, functional annotation and the substitution model used in phylogenetic analyses all refer to Nicholls et al. (2015).
Data
Detailed chemical methods for construction of a chemical similarity matrix.
Data
Parafit analysis output for sawfly and Inga phylogenies, for sawfly MOTUs in the family Argidae. (B) Parafit analysis of concordance between sawfly phylogeny and Inga chemogram. In (A) and (B) herbivore-Inga associations that are identified as individually significant are highlighted in yellow.
Data
Results of MOTU identification analyses of Inga- and Zygia-feeding sawflies, using a 645 bp fragment of the mitochondrial COI DNA barcoding region for (a) jMOTU and (b) ABGD.
Data
Phylogenetic relationships for the gene CO1 among the Inga-feeding sawfly MOTUs and a panel of voucher sequences for sawflies in the families Argidae, Pergidae (sister group to Argidae; Malm and Nyman, 2015) and Tenthredinidae. The tree shown is a majority-rule consensus tree constructed in MrBayes, using substitutions modeled as GTR+I+G for each o...
Data
Metadata for additional reference sawfly sequences, with species name, country of origin, Genbank accession numbers for COI and PGD gene fragments, and source reference.
Article
Full-text available
Coursetia caribaea is geographically and morphologically the most variable species in the genus Coursetia and in the tribe Robinieae (Leguminosae, Papilionoideae). Because of potentially undetected species, we assessed the phylogenetic relationships among the eight taxonomic varieties of C. caribaea. Sampling included nuclear ribosomal internal tra...