Charles C Davis

Harvard University | Harvard · Department of Organismic and Evolutionary Biology

The use of herbaria for science and conservation is enabling greatly enhanced scopes and scales of discovery, exploration and protection of biodiversity. The availability of digital, open-access herbarium data is, perhaps counter-intuitively, expanding the use of physical collections by researchers who use digital collections to find specimens and...

Forecasting the impacts of changing climate on the phenology of plant populations is essential for anticipating and managing potential ecological disruptions to biotic communities. Herbarium specimens enable assessments of plant phenology across broad spatiotemporal scales. However, specimens are collected opportunistically, and it is unclear wheth...

The use of herbaria for science and conservation is revolutionizing the discovery, exploration, and protection of biodiversity at unprecedented scopes and scales. The Global Metaherbarium—a digitally interlinked, open-access resource—is stimulating these efforts and helping to facilitate massive investigations that utilize aggregated digital deriva...

Anthropogenetic climate change has caused range shifts among many species. Species distribution models (SDMs) are used to predict how species ranges may change in the future. However, most SDMs rarely consider how climate‐sensitive traits, such as phenology, which affect individuals' demography and fitness, may influence species' ranges. Using > 12...

Last month, Duke University in North Carolina announced that it was shuttering its herbarium. The collection consists of nearly 1 million specimens representing the most comprehensive and historic set of plants from the southeastern United States. It also includes extensive holdings from other regions of the world, especially Mexico, Central Americ...

Species identification using DNA barcodes has revolutionized biodiversity sciences and society at large. However, conventional barcoding methods do not reflect genomic complexity, may lack sufficient variation, and rely on limited genomic loci that are not universal across the Tree of Life. Here, we develop a novel barcoding method that uses except...

Phenology varies widely over space and time because of its sensitivity to climate. However, whether phenological variation is primarily generated by rapid organismal responses (plasticity) or local adaptation remains unresolved. Here we used 1,038,027 herbarium specimens representing 1,605 species from the continental United States to measure flowe...

Bees are the most significant pollinators of flowering plants. This partnership began ca. 120 million years ago, but the uncertainty of how and when bees spread across the planet has greatly obscured investigations of this key mutualism. We present a novel analysis of bee biogeography using extensive new genomic and fossil data to demonstrate that...

Species distribution models (SDMs) have been central for documenting the relationship between species' geographic ranges and environmental conditions for more than two decades. However, the vast majority of SDMs rarely consider functional traits, such as phenology, which strongly affect species' demography and fitness. Using >120,000 herbarium spec...

Phenology varies widely over space and time because of its sensitivity to climate. However, whether phenological variation is primarily generated by rapid organismal responses (i.e., plasticity) or local adaptation remains unresolved. Here, we used 1,038,027 herbarium specimens representing 1,605 species to measure flowering time sensitivity to tem...

Herbarium collections shape our understanding of Earth’s flora and are crucial for addressing global change issues. Their formation, however, is not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparative...

Forecasting the impacts of changing climate on the phenology of plant populations is essential for anticipating and managing potential ecological disruptions to biotic communities. Herbarium specimens enable assessments of plant phenology across broad spatiotemporal scales. However, specimens are collected opportunistically, and it is unclear wheth...

Urbanization can affect the timing of plant reproduction (i.e. flowering and fruiting) and associated ecosystem processes. However, our knowledge of how plant phenology responds to urbanization and its associated environmental changes is limited. Herbaria represent an important, but underutilized source of data for investigating this question. We h...

Cystocloniacae is a highly diverse family of Rhodophyta, including species of ecological and economic importance, whose phylogeny remains largely unresolved. Species delimitation is unclear, particularly in the most speciose genus, Hypnea, and cryptic diversity has been revealed by recent molecular assessments, especially in the tropics. Here, we c...

Premise: Quantifying how closely related plant species differ in susceptibility to insect herbivory is important for understanding the variation in evolutionary pressures on plant functional traits. However, empirically measuring in situ variation in herbivory spanning the geographic range of a plant-insect complex is logistically difficult. Recen...

The genus Keraunea was recently described in the Convolvulaceae Juss. family. Two species are currently recognised, both from Brazil. Molecular sequence data using three commonly applied DNA markers (matK, rbcL and the nuclear ribosomal Internal Transcribed Spacer) show that neither species is correctly placed in Convolvulaceae but indicates that t...

Resurrecting extinct species is a fascinating and challenging idea for scientists and the general public. Whereas some theoretical progress has been made for animals, the resurrection of extinct plants (de-extinction sensu lato) is a relatively recently discussed topic. In this context, the term ‘de-extinction’ is used sensu lato to refer to the re...

Plant phenology has been shifting dramatically in response to climate change, a shift that may have significant and widespread ecological consequences. Of particular concern are tropical biomes, which represent the most biodiverse and imperilled regions of the world. However, compared to temperate floras, we know little about phenological responses...

Radiations are especially important for generating species biodiversity in mountainous ecosystems. The contribution of hybridization to such radiations has rarely been examined. Here, we use extensive genomic data to test whether hybridization was involved in evolutionary radiation within Rhododendron subgenus Hymenanthes, whose members show strong...

The ~400 million specimens deposited across ~3000 herbaria are essential for: (i) understanding where plants have lived in the past, (ii) forecasting where they may live in the future, and (iii) delineating their conservation status. An open access ‘global metaherbarium’ is emerging as these specimens are digitized, mobilized, and interlinked onlin...

The genus Keraunea was recently described in the Convolvulaceae Juss. family. Two species are currently recognised, both from Brazil. Molecular sequence data using three commonly applied DNA markers (matK, rbcL and the nuclear ribosomal Internal Transcribed Spacer) show that neither species is correctly placed in Convolvulaceae but indicates that t...

Plant phenology has been shifting dramatically in response to climate change, a shift that may have significant and widespread ecological consequences. Of particular concern are tropical biomes, which represent the most biodiverse and imperiled regions of the world. However, compared to temperate floras, we know little about phenological responses...

Wetlands are highly productive ecosystems that host unique biota and provide vital ecosystem services. Despite their critical importance, we still lack a fundamental understanding of factors controlling species suitability and climate change impacts in wetlands essential to conserving these imperiled ecosystems in the face of anthropogenic threats....

Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes, and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventuall...

Earth's most speciose biomes are in the tropics, yet tropical plant phenology remains poorly understood. Tropical phenological data are comparatively scarce and viewed through the lens of a 'temperate phenological paradigm' expecting phenological traits to respond to strong, predictably annual shifts in climate (e.g., between subfreezing and frost-...

Premise: The application of high-throughput sequencing, especially to herbarium specimens, is rapidly accelerating biodiversity research. Low-coverage sequencing of total genomic DNA (genome skimming) is particularly promising and can simultaneously recover the plastid, mitochondrial, and nuclear ribosomal regions across hundreds of species. Here,...

The widespread digitization of natural history collections, combined with novel tools and approaches is revolutionizing biodiversity science. The ‘extended specimen’ concept advocates a more holistic approach in which a specimen is framed as a diverse stream of interconnected data. Herbarium specimens that by their very nature capture multispecies...

Flowering plants (angiosperms) dominate our planet and sustain all life on Earth. However, evolutionary relationships among the angiosperm lineages that diverged early – Amborellales, Nymphaeales, Austrobaileyales and Mesangiospermae, which further comprises monocots and other four clades – have remained highly disputed likely because of their rapi...

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...

Premise of the study: The application of high throughput sequencing, especially to herbarium specimens, is greatly accelerating biodiversity research. Among various techniques, low coverage Illumina sequencing of total genomic DNA (genome skimming) can simultaneously recover the plastid, mitochondrial, and nuclear ribosomal regions across hundreds...

Herbarium collections shape our understanding of the world's flora and are crucial for addressing global change and biodiversity conservation. The formation of such natural history collections, however, are not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in n...

Interactions between species can influence successful reproduction, resulting in reproductive character displacement, where the similarity of reproductive traits – such as flowering time – among close relatives growing together differ from when growing apart. Evidence for the overall prevalence and direction of this phenomenon, and its stability un...

Gracilariales is a highly diverse, widely distributed clade of red algae (Rhodophyta). Aside from their ecological importance, species of Gracilariales provide important sources of agarans and possess bioactive compounds with medicinal and pharmaceutical use. Recent phylogenetic analyses from a small number of genes have greatly advanced our knowle...

PREMISE: Quantifying how closely related plant species differ in susceptibility to insect herbivory is important for our understanding of variation in plant-insect ecological interactions and evolutionary pressures on plant functional traits. However, empirically measuring in situ variation in herbivory over the entire geographic range where a plan...

A review of parasitic plant diversity and outstanding disjunct distributions according to an updated functional classification based on these plants’ life cycles.

Desiccation tolerance was a key trait that allowed plants to colonize land. However, little is known about the transition from desiccation tolerant non-vascular plants to desiccation sensitive vascular ones. Filmy ferns (Hymenophyllaceae) represent a useful system to investigate how water-stress strategies differ between non-vascular and vascular s...

The tea family (Theaceae) has a highly unusual amphi-Pacific disjunct distribution: most extant species in the family are restricted to subtropical evergreen broadleaf forests in East Asia, while a handful of species occur exclusively in the subtropical and tropical Americas. Here we used an approach that integrates the rich fossil evidence of this...

Premise: A subset of parasitic plants bear extremely reduced features and grow nearly entirely within their hosts. Until recently, most of these endoparasites were thought to represent a single clade united by their reduced morphology. Current phylogenetic understanding contradicts this assumption and indicates these plants represent distantly rel...

Tovomita is aNeotropical clade of Clusiaceae that includes 52 species widely distributed throughout the Amazon,Atlantic, Antilles, and Chocoan/southern Mesoamerican rainforests. Species-level relationships within Tovomita remain largely unexplored, thus hindering our understanding of their biogeography and the evolution of key morphological charact...

Species interactions drive ecosystem processes and are a major focus of global change research. Among the most consequential interactions expected to shift with climate change are those between insect herbivores and plants, both of which are highly sensitive to temperature. Insect herbivores and their host plants display varying levels of synchrony...

Desiccation tolerance was a key trait that allowed plants to colonize land. However, little is known about the transition from desiccation tolerant non-vascular plants to desiccation sensitive vascular ones. Filmy ferns (Hymenophyllaceae) represent a useful system to investigate how water-stress strategies differ between non-vascular and vascular s...

The digitization of herbarium collections is greatly transforming plant biodiversity science, yet most herbarium data remain inaccessible. Here, we present a novel, single‐user photostation and associated workflow for efficiently mobilizing herbarium specimens. Our apparatus represents a significant improvement to existing technology and is scalabl...

Despite more than 2,000-fold variation in genome size, key features of genome architecture are largely conserved across angiosperms. Parasitic plants have elucidated the many ways in which genomes can be modified, yet we still lack comprehensive genome data for species that represent the most extreme form of parasitism. Here, we present the highly...

The development of next‐generation sequencing technologies allows researchers to address complex problems in species delimitation, particularly for non‐model organisms. The taxonomic status of North American Nyssa species has long been debated and remains controversial. To elucidate the genetic structure and phylogenetic relationships of the five c...

The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal b...

Subsequent to our recent publication honoring William R. Anderson (Davis et al., 2020), we discovered the publication of an obscure monotypic genus of algae, Andersoniella F. Schmitz (1897: 520), that is nowadays recognized as a synonym of Leptocladia J.Agardh (1892: 95) (Schneider & Wynne, 2007). This immediately rendered our name a later homonym...

The digitization and online mobilization of herbarium specimens has greatly facilitated their access and helped ignite a revolution in the biodiversity sciences (Drew et al., 2017; Hedrick et al., 2020; Nelson et al., 2015; Soltis, 2017; Sweeney et al., 2018; Thiers et al., 2016). These efforts have mobilized millions of specimens with significant...

Kozlov and colleagues ¹ call into question the application of herbarium specimens to quantify historical patterns of herbivory 2–5 . It is already widely appreciated that collectors of herbarium specimens may tend to avoid insect damage, thus making herbivory estimates from herbarium specimens potentially down-biased ² . However, Kozlov et al . add...

Invasive species are a major threat to biodiversity and ecosystem function. Thus, understanding their spread and ecological impacts is critical for management and control. Strawberry guava (Psidium cattleianum Sabine) is an aggressive invader across the tropics and has been rapidly spreading throughout the eastern rainforests of Madagascar. However...

Interactions between species can influence access to resources and successful reproduction. One possible outcome of such interactions is reproductive character displacement. Here, the similarity of reproductive traits - such as flowering time - among close relatives growing in sympatry differ more so than when growing apart. However, evidence for t...

Phenology—the timing of life-history events—is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current practice of manually harvesting data from individual specime...

Machine learning (ML) has great potential to drive scientific discovery by harvesting data from images of herbarium specimens-preserved plant material curated in natural history collections-but ML techniques have only recently been applied to this rich resource. ML has particularly strong prospects for the study of plant phenological events such as...

Morphological and molecular investigations of the galphimioid clade in the angiosperm family Malpighiaceae revealed that three species previously assigned to Lophanthera are more closely allied with Spachea. These species are transferred to the newly described genus Andersoniella and include A. hammelii, A. marcelae, and A. spruceana, the type spec...

Phenology, the timing of life-history events, is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current practice of manually harvesting data from individual speci...

Intergeneric relationships of the Beilschmiedia group (Lauraceae) remain unresolved, hindering our understanding of their classification and evolutionary diversification. To remedy this, we sequenced and assembled complete plastid genomes (plastomes) from 25 species representing five genera spanning most major clades of Beilschmiedia and close rela...

Though substantial effort has gone into predicting how global climate change will impact biodiversity patterns, the scarcity of taxon‐specific information has hampered the efficacy of these endeavors. Further, most studies analyzing spatiotemporal patterns of biodiversity focus narrowly on species richness. We apply machine learning approaches to a...

The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal b...

The expansion of angiosperm‐dominated forests in the Cretaceous and early Cenozoic had a profound effect on terrestrial biota by creating novel ecological niches. The majority of modern fern lineages are hypothesized to have arisen in response to this expansion, particularly fern epiphytes that radiated into the canopy. Recent evidence, however, su...

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...

The same technological tools that spread misinformation and influence elections are now taking aim at our natural world. Misinformation campaigns on social media are particularly rampant and troubling in Brazil. In the past year, backers of Jair Bolsonaro’s government burnt vast tracts of the Amazon rainforest to support large-scale agribusiness, f...

For more than 225 million y, all seed plants were woody trees, shrubs, or vines. Shortly after the origin of angiosperms ∼140 million y ago (MYA), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium, the meristematic population of cells that produces secondary x...

Angiosperms represent one of the most spectacular terrestrial radiations on the planet¹, but their early diversification and phylogenetic relationships remain uncertain2–5. A key reason for this impasse is the paucity of complete genomes representing early-diverging angiosperms. Here, we present high-quality, chromosomal-level genome assemblies of...

Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization—the conversion of specimen data into accessible digital content—has greatly expanded the use of NHC collections across a diversity of disciplines....

For more than 225 million years, all seed plants were woody trees, shrubs, or vines (1–4). Shortly after the origin of angiosperms ~135 million years ago (MYA) (5), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium (6), the meristematic population of cells tha...

The plastid genomes (plastomes) of non-photosynthetic plants generally undergoes gene loss and pseudogenization. Despite massive plastomes reported in different parasitism types of the broomrape family (Orobanchaceae), more plastomes representing different degradation patterns in a single genus are expected to be explored. Here, we sequenced and as...

The historical course of evolutionary diversification shapes the current distribution of biodiversity, but the main forces constraining diversification are unclear. We unveil the evolutionary structure of tree species diversity across the Americas to assess whether an inability to move (dispersal limitation) or to evolve (niche conservatism) is the...

Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization–the conversion of specimen data into accessible digital content–has greatly expanded the use of NHC collections across a diversity of disciplines....

Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization–the conversion of specimen data into accessible digital content–has greatly expanded the use of NHC collections across a diversity of disciplines....

In the version of this Article originally published, the rate of change plotted in Figure 2 was incorrect because of a coding error. The corrected figure is shown below. In the original Figure 2 legend, the onset of flowering slope was given as ‘0.99, 95% CI: 0.90–1.08’, the cessation of flowering slope was given as ‘1.02, 95% CI: 0.91–1.13’, and t...

Clusieae is an exclusively Neotropical tribe in the family Clusiaceae sensu stricto. Although tribes within Clusiaceae are morphologically and phylogenetically well-delimited, resolution among genera within these tribes remains elusive. The tribe Clusieae includes an estimated ∼500 species distributed among five genera: Chrysochlamys, Clusia, Dysto...