A new nuclear phylogeny of the tea family (Theaceae) unravels rapid radiations in genus Camellia

Molecular analyses of rapidly radiating groups often reveal incongruence between gene trees. This mainly results from incomplete lineage sorting, introgression, and gene tree estimation error, which complicate the estimation of phylogenetic relationships. In this study, we reconstruct the phylogeny of Theaceae using 348 nuclear loci from 68 individuals and two outgroup taxa. Sequence data were obtained by target enrichment using the recently released Angiosperm 353 universal probe set applied to herbarium specimens. The robustness of the topologies to variation in data quality was established under a range of different filtering schemes, using both coalescent and concatenation approaches. Our results confirmed most of the previously hypothesized relationships among tribes and genera, while clarifying additional interspecific relationships within the rapidly radiating genus Camellia. We recovered a remarkably high degree of gene tree heterogeneity indicative of rapid radiation in the group and observed cytonuclear conflicts, especially within Camellia. This was especially pronounced around short branches, which we primarily associate with gene tree estimation error. Our analysis also indicates that incomplete lineage sorting (ILS) contributed to gene-tree conflicts and accounted for approximately 14 % of the explained variation, whereas inferred introgression levels were low. Our study advances the understanding of the evolution of this important plant family and provides guidance on the application of target capture methods and the evaluation of key processes that influence phylogenetic discordances.

Pleistocene glaciation advances the cryptic speciation of Stellera chamaejasme L. in a major biodiversity hotspot

The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate change. The high species diversity in this mountain system has long been attributed to a complex set of factors, and recent large-scale macroevolutionary investigations have placed a broad timeline on plant diversification that stretches from 10 million years ago (Mya) to the present. Despite our increasing understanding of the temporal mode of speciation, finer-scale population-level investigations are lacking to better refine these temporal trends and illuminate the abiotic and biotic influences of cryptic speciation. This is largely due to the dearth of organismal sampling among closely related species and populations, spanning the incredible size and topological heterogeneity of this region. Our study dives into these evolutionary dynamics of speciation using genomic and eco-morphological data of Stellera chamaejasme L. We identified four previously unrecognized cryptic species having indistinct morphological traits and large metapopulation of evolving lineages, suggesting a more recent diversification (~2.67-0.90 Mya), largely influenced by Pleistocene glaciation and biotic factors. These factors likely influenced allopatric speciation and advocated cyclical warming-cooling episodes along elevational gradients during the Pleistocene. The study refines the evolutionary timeline to be much younger than previously implicated and raises the concern that projected future warming may influence the alpine species diversity, necessitating increased conservation efforts.

Incorporating plant phenological responses into species distribution models reduces estimates of future species loss and turnover

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 > 120 000 herbarium specimens representing 360 plant species distributed across the eastern United States, we developed a novel 'phenology-informed' SDM that integrates phenological responses to changing climates. We compared the ranges of each species forecast by the phenology-informed SDM with those from conventional SDMs. We further validated the modeling approach using hindcasting. When examining the range changes of all species, our phenology-informed SDMs forecast less species loss and turnover under climate change than conventional SDMs. These results suggest that dynamic phenological responses of species may help them adjust their ecological niches and persist in their habitats as the climate changes. Plant phenology can modulate species' responses to climate change, mitigating its negative effects on species persistence. Further application of our framework will contribute to a generalized understanding of how traits affect species distributions along environmental gradients and facilitate the use of trait-based SDMs across spatial and taxonomic scales.

Collections are truly priceless

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 America, and the West Indies. Duke plans to disperse these samples to other institutions for use or storage over the next 2 to 3 years, but this decision reflects a lack of awareness by academia that such collections are being leveraged as never before. With modern technologies spanning multiple fields of study, the holdings in herbaria and other natural history collections are not only facilitating a deeper and broader understanding of the past and present world but are also providing tools to meet both known and unforeseen challenges facing humanity. Science and society can hardly risk the loss of such an important resource.

Plasticity and not adaptation is the primary source of temperature-mediated variation in flowering phenology in North America

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 flowering-time sensitivity to temperature over time (Stime) and space (Sspace). By comparing these estimates, we inferred how adaptation and plasticity historically influenced phenology along temperature gradients and how their contributions vary among species with different phenology and native climates and among ecoregions differing in species composition. Parameters Sspace and Stime were positively correlated (r = 0.87), of similar magnitude and more frequently consistent with plasticity than adaptation. Apparent plasticity and adaptation generated earlier flowering in spring, limited responsiveness in late summer and delayed flowering in autumn in response to temperature increases. Nonetheless, ecoregions differed in the relative contributions of adaptation and plasticity, from consistently greater importance of plasticity (for example, southeastern United States plains) to their nearly equal importance throughout the season (for example, Western Sierra Madre Piedmont). Our results support the hypothesis that plasticity is the primary driver of flowering-time variation along temperature gradients, with local adaptation having a widespread but comparatively limited role.

Medicinal plants meet modern biodiversity science

Plants have been an essential source of human medicine for millennia. In this review, we argue that a holistic, interdisciplinary approach to the study of medicinal plants that combines methods and insights from three key disciplines - evolutionary ecology, molecular biology/biochemistry, and ethnopharmacology - is poised to facilitate new breakthroughs in science, including pharmacological discoveries and rapid advancements in human health and well-being. Such interdisciplinary research leverages data and methods spanning space, time, and species associated with medicinal plant species evolution, ecology, genomics, and metabolomic trait diversity, all of which build heavily on traditional Indigenous knowledge. Such an interdisciplinary approach contrasts sharply with most well-funded and successful medicinal plant research during the last half-century, which, despite notable advancements, has greatly oversimplified the dynamic relationships between plants and humans, kept hidden the larger human narratives about these relationships, and overlooked potentially important research and discoveries into life-saving medicines. We suggest that medicinal plants and people should be viewed as partners whose relationship involves a complicated and poorly explored set of (socio-)ecological interactions including not only domestication but also commensalisms and mutualisms. In short, medicinal plant species are not just chemical factories for extraction and exploitation. Rather, they may be symbiotic partners that have shaped modern societies, improved human health, and extended human lifespans.

Complex climate-mediated effects of urbanization on plant reproductive phenology and frost risk

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 harnessed phenological data from herbarium specimens representing 200 plant species collected across 120 yr from the eastern US to investigate the spatiotemporal effects of urbanization on flowering and fruiting phenology and frost risk (i.e. time between the last frost date and flowering). Effects of urbanization on plant reproductive phenology varied significantly in direction and magnitude across species ranges. Increased urbanization led to earlier flowering in colder and wetter regions and delayed fruiting in regions with wetter spring conditions. Frost risk was elevated with increased urbanization in regions with colder and wetter spring conditions. Our study demonstrates that predictions of phenological change and its associated impacts must account for both climatic and human effects, which are context dependent and do not necessarily coincide. We must move beyond phenological models that only incorporate temperature variables and consider multiple environmental factors and their interactions when estimating plant phenology, especially at larger spatial and taxonomic scales.

The evolutionary history of bees in time and space

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 bees originated in Western Gondwana (Africa and South America). Bees likely originated in the Early Cretaceous, shortly before the breakup of Western Gondwana, and the early evolution of any major bee lineage is associated with either the South American or African land masses. Subsequently, bees colonized northern continents via a complex history of vicariance and dispersal. The notable early absences from large landmasses, particularly in Australia and India, have important implications for understanding the assembly of local floras and diverse modes of pollination. How bees spread around the world from their hypothesized Southern Hemisphere origin parallels the histories of numerous flowering plant clades, providing an essential step to studying the evolution of angiosperm pollination syndromes in space and time.

The colonial legacy of herbaria

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 comparatively less attention. While it has been noted that the majority of plant specimens are housed in the Global North, the extent and magnitude of this disparity have not been quantified. Here we examine the colonial legacy of botanical collections, analysing 85,621,930 specimen records and assessing survey responses from 92 herbarium collections across 39 countries. We find an inverse relationship between where plant diversity exists in nature and where it is housed in herbaria. Such disparities persist across physical and digital realms despite overt colonialism ending over half a century ago. We emphasize the need for acknowledging the colonial history of herbarium collections and implementing a more equitable global paradigm for their collection, curation and use.

Phylogenomics and taxon-rich phylogenies of new and historical specimens shed light on the systematics of Hypnea (Cystocloniaceae, Rhodophyta)

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 carried out the first phylogenomic investigation of Cystocloniaceae, focused on the genus Hypnea, inferred from chloroplast and mitochondrial genomes including taxa sampled from new and historical collections. In this work, molecular synapomorphies (gene losses, InDels and gene inversions) were identified to better characterize clades in our congruent organellar phylogenies. We also present taxon-rich phylogenies based on plastid and mitochondrial markers. Molecular and morphological comparisons of historic collections with contemporary specimens revealed the need for taxonomic updates in Hypnea, the synonymization of H. marchantae to a later heterotypic synonym of H. cervicornis and the description of three new species: H. davisiana sp. nov., H. djamilae sp. nov. and H. evaristoae sp. nov.

Herbarium specimens reveal herbivory patterns across the genus Cucurbita

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. Recently, new methods have been developed using herbarium specimens to investigate patterns in plant-insect symbioses across large geographic scales. Such investigations provide insights into how accelerated anthropogenic changes may impact plant-insect interactions that are of ecological or agricultural importance.

METHODS

Here, we analyze 274 pressed herbarium samples to investigate variation in herbivory damage in 13 different species of the economically important plant genus Cucurbita (Cucurbitaceae). This collection is composed of specimens of wild, undomesticated Cucurbita that were collected from across their native range, and Cucurbita cultivars collected from both within their native range and from locations where they have been introduced for agriculture in temperate North America.

RESULTS

Herbivory is common on individuals of all Cucurbita species collected throughout their geographic ranges. However, estimates of herbivory varied considerably among individuals, with mesophytic species accruing more insect damage than xerophytic species, and wild specimens having more herbivory than specimens collected from human-managed habitats.

CONCLUSIONS

Our study suggests that long-term evolutionary changes in habitat from xeric to mesic climates and wild to human-managed habitats may mediate the levels of herbivory pressure from coevolved herbivores. Future investigations into the potential factors that contribute to herbivory may inform the management of domesticated crop plants and their insect herbivores.

The herbarium of the future

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 online. This virtual biodiversity resource is attracting new users who are accelerating traditional applications of herbaria and generating basic and applied scientific innovations, including e-monographs and floras produced by diverse, interdisciplinary, and inclusive teams; robust machine-learning algorithms for species identification and phenotyping; collection and synthesis of ecological trait data at large spatiotemporal and phylogenetic scales; and exhibitions and installations that convey the beauty of plants and the value of herbaria in addressing broader societal issues.

Pervasive hybridization during evolutionary radiation of Rhododendron subgenus Hymenanthes in mountains of southwest China

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 geographic isolation in the mountains of southwest China. We sequenced genomes for 143 species of this subgenus and 93 species of four other subgenera, and found that Hymenanthes was monophyletic and radiated during the late Oligocene to middle Miocene. Widespread hybridization events were inferred within and between the identified clades and subclades. This suggests that hybridization occurred both early and late during diversification of subgenus Hymenanthes, although the extent to which hybridization, speciation through mixing-isolation-mixing or hybrid speciation, accelerated the diversification needs further exploration. Cycles of isolation and contact in such and other montane ecosystems may have together promoted species radiation through hybridization between diverging populations and species. Similar radiation processes may apply to other montane floras in this region and elsewhere.

Selecting the best candidates for resurrecting extinct-in-the-wild plants from herbaria

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 resurrection of 'extinct in the wild' species from seeds or tissues preserved in herbaria, as we acknowledge the current impossibility of knowing a priori whether a herbarium seed is alive and can germinate. In plants, this could be achieved by germinating or in vitro tissue-culturing old diaspores such as seeds or spores available in herbarium specimens. This paper reports the first list of plant de-extinction candidates based on the actual availability of seeds in herbarium specimens of globally extinct plants. We reviewed globally extinct seed plants using online resources and additional literature on national red lists, resulting in a list of 361 extinct taxa. We then proposed a method of prioritizing candidates for seed-plant de-extinction from diaspores found in herbarium specimens and complemented this with a phylogenetic approach to identify species that may maximize evolutionarily distinct features. Finally, combining data on seed storage behaviour and longevity, as well as specimen age in the novel 'best de-extinction candidate' score (DEXSCO), we identified 556 herbarium specimens belonging to 161 extinct species with available seeds. We expect that this list of de-extinction candidates and the novel approach to rank them will boost research efforts towards the first-ever plant de-extinction.

Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication

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 eventually lost. When speciation occurs shortly after WGD; however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs–paralogous genes mistakenly identified as orthologs because they are present in single copies within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) are only recently gaining empirical attention in the phylogenomics community. Moreover, few studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era. [Coalescent method; concatenation method; incomplete lineage sorting; pseudoorthologs; single-copy gene; whole-genome duplication.]

PhyloHerb: A high-throughput phylogenomic pipeline for processing genome skimming data

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, we introduce PhyloHerb, a bioinformatic pipeline to efficiently assemble phylogenomic data sets derived from genome skimming.

METHODS AND RESULTS

PhyloHerb uses either a built-in database or user-specified references to extract orthologous sequences from all three genomes using a BLAST search. It outputs FASTA files and offers a suite of utility functions to assist with alignment, partitioning, concatenation, and phylogeny inference. The program is freely available at https://github.com/lmcai/PhyloHerb/.

CONCLUSIONS

We demonstrate that PhyloHerb can accurately identify genes using a published data set from Clusiaceae. We also show via simulations that our approach is effective for highly fragmented assemblies from herbarium specimens and is scalable to thousands of species.

Phenological displacement is uncommon among sympatric angiosperms

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 under environmental change, remains untested across large scales. Using the power of crowdsourcing, we gathered phenological information from over 40 000 herbarium specimens, and investigated displacement in flowering time across 110 animal-pollinated species in the eastern USA. Overall, flowering time displacement is not common across large scales. However, displacement is generally greater among species pairs that flower close in time, regardless of direction. Furthermore, with climate change, the flowering times of closely related species are predicted, on average, to shift further apart by the mid-21^st century. We demonstrate that the degree and direction of phenological displacement among co-occurring closely related species pairs varies tremendously. However, future climate change may alter the differences in reproductive timing among many of these species pairs, which may have significant consequences for species interactions and gene flow. Our study provides one promising path towards understanding how the phenological landscape is structured and may respond to future environmental change.

Widespread homogenization of plant communities in the Anthropocene

Native biodiversity decline and non-native species spread are major features of the Anthropocene. Both processes can drive biotic homogenization by reducing trait and phylogenetic differences in species assemblages between regions, thus diminishing the regional distinctiveness of biotas and likely have negative impacts on key ecosystem functions. However, a global assessment of this phenomenon is lacking. Here, using a dataset of >200,000 plant species, we demonstrate widespread and temporal decreases in species and phylogenetic turnover across grain sizes and spatial extents. The extent of homogenization within major biomes is pronounced and is overwhelmingly explained by non-native species naturalizations. Asia and North America are major sources of non-native species; however, the species they export tend to be phylogenetically close to recipient floras. Australia, the Pacific and Europe, in contrast, contribute fewer species to the global pool of non-natives, but represent a disproportionate amount of phylogenetic diversity. The timeline of most naturalisations coincides with widespread human migration within the last ~500 years, and demonstrates the profound influence humans exert on regional biotas beyond changes in species richness.

Human-driven movements and extinctions of species have made plant communities across biomes more homogenous. Here the authors quantify plant vascular species and phylogenetic homogenization across the globe, finding that non-native species naturalisations have been a major driver.

Life history, diversity, and distribution in parasitic flowering plants

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

Ecophysiological differentiation between life stages in filmy ferns (Hymenophyllaceae)

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 stages within a single organism because they have vascularized sporophytes and nonvascular gametophytes that are each capable of varying degrees of desiccation tolerance. To explore this, we surveyed sporophytes and gametophytes of 19 species (22 taxa including varieties) of filmy ferns on Moorea (French Polynesia) and used chlorophyll fluorescence to measure desiccation tolerance and light responses. We conducted phylogenetically informed analyses to identify differences in physiology between life stages and growth habits. Gametophytes had similar or less desiccation tolerance (ability to recover from 2 days desiccation at - 86 MPa) and lower photosynthetic optima (maximum electron transport rate of photosystem II and light level at 95% of that rate) than sporophytes. Epiphytes were more tolerant of desiccation than terrestrial species in both life stages. Despite their lack of greater physiological tolerances, gametophytes of several species occurred over a wider elevational range than conspecific sporophytes. Our results demonstrate that filmy fern gametophytes and sporophytes differ in their physiology and niche requirements, and point to the importance of microhabitat in shaping the evolution of water-use strategies in vascular plants.

Phytogeographic history of the Tea family inferred through high-resolution phylogeny and fossils

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 group with phylogenies in biogeographic analysis to study the processes behind this distribution pattern. We first combined genome-skimming sequencing with existing molecular data to build a robust species-level phylogeny for c.140 Theaceae species, resolving most important unclarified relationships. We then developed an empirical Bayesian method to incorporate distribution evidence from fossil specimens into historical biogeographic analyses and used this method to account for the spatiotemporal history of Theaceae fossils. We compared our method with an alternative Bayesian approach and show that it provides consistent results while significantly reduces computational demands which allows analyses of much larger datasets. Our analyses revealed a circumboreal distribution of the family from the early Cenozoic to the Miocene and inferred repeated expansions and retractions of the modelled distribution in the Northern Hemisphere, suggesting that the current Theaceae distribution could be the remnant of a larger continuous distribution associated with the boreotropical forest that has been hypothesized to occupy most of the northern latitudes in the early Cenozoic. These results contradict with studies that only considered current species distributions and showcase the necessity of integrating fossil and molecular data in phylogeny-based parametric biogeographic models to improve the reliability of inferred biogeographical events.

Phenological sensitivity to temperature mediates herbivory

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 that could be disrupted or enhanced by climate change, yet empirical data on changes in synchrony are lacking. Using evidence of herbivory on herbarium specimens collected from the northeastern United States and France from 1900 to 2015, we provide evidence that plant species with temperature-sensitive phenologies experience higher levels of insect damage in warmer years, while less temperature-sensitive, co-occurring species do not. While herbivory might be mediated by interactions between warming and phenology through multiple pathways, we suggest that warming might lengthen growing seasons for phenologically sensitive plant species, exposing their leaves to herbivores for longer periods of time in warm years. We propose that elevated herbivory in warm years may represent a previously underappreciated cost to phenological tracking of climate change over longer timescales.

Striking developmental convergence in angiosperm endoparasites

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 related clades, thus offering an opportunity to examine convergence among plants with this life history.

METHODS

We sampled species from Apodanthaceae, Cytinaceae, Mitrastemonaceae, and Rafflesiaceae spanning a range of developmental stages. To provide a broader comparative framework, Santalaceae mistletoes with a similar lifestyle were also analyzed. Microtomography and microscopy were used to analyze growth patterns and the ontogeny of host-parasite vascular connections.

RESULTS

Apodanthaceae, Cytinaceae, Mitrastemonaceae, and Rafflesiaceae species demonstrated a common development characterized by late cell differentiation. These species were also observed to form direct connections to host vessels and to cause severe alterations of host xylem development. Apodanthaceae and Rafflesiaceae species were additionally observed to form sieve elements, which connect with the host phloem. Endophytic Santalaceae species demonstrated a dramatically different developmental pattern, featuring early cell differentiation and tissue organization, and little effect on host anatomy and cambial activity.

CONCLUSIONS

Our results illuminate two distinct developmental trajectories in endoparasites. One involves the retention of embryonic characteristics and late connection with host vessels, as demonstrated in species of Apodanthaceae, Cytinaceae, Mitrastemonaceae, and Rafflesiaceae. The second involves tissue specialization and early connection with host xylem, as exemplified by Santalaceae species. These differences are hypothesized to be related to the absence/presence of photosynthesis in these plants.

The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales

The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent 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 branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes 9 of the top 10 most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0$\%$, 34.8$\%$, and 21.4$\%$ of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution. [Coalescent; concatenation; flanking region; hybrid enrichment, introgression; phylogenomics; rapid radiation, triplet frequency.].

Life in the canopy: community trait assessments reveal substantial functional diversity among fern epiphytes

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, suggests that epiphytism does not correlate with increased diversification rates in ferns, calling into question the role of the canopy habitat in fern evolution. To understand the role of the canopy in structuring fern community diversity, we investigated functional traits of fern sporophytes and gametophytes across a broad phylogenetic sampling on the island of Moorea, French Polynesia, including > 120 species and representatives of multiple epiphytic radiations. While epiphytes showed convergence in small size and a higher frequency of noncordate gametophytes, they showed greater functional diversity at the community level relative to terrestrial ferns. These results suggest previously overlooked functional diversity among fern epiphytes, and raise the hypothesis that while the angiosperm canopy acted as a complex filter that restricted plant size, it also facilitated diversification into finely partitioned niches. Characterizing these niche axes and adaptations of epiphytic ferns occupying them should be a priority for future pteridological research.

Machine learning predicts large scale declines in native plant phylogenetic diversity

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 comprehensive vascular plant database for the United States and generate predictive models of regional plant taxonomic and phylogenetic diversity in response to a wide range of environmental variables. We demonstrate differences in predicted patterns and potential drivers of native vs nonnative biodiversity. In particular, native phylogenetic diversity is likely to decrease over the next half century despite increases in species richness. We also identify that patterns of taxonomic diversity can be incongruent with those of phylogenetic diversity. The combination of macro-environmental factors that determine diversity likely varies at continental scales; thus, as climate change alters the combinations of these factors across the landscape, the collective effect on regional diversity will also vary. Our study represents one of the most comprehensive examinations of plant diversity patterns to date and demonstrates that our ability to predict future diversity may benefit tremendously from the application of machine learning.

A New Method for Counting Reproductive Structures in Digitized Herbarium Specimens Using Mask R-CNN

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 specimens, however, greatly restricts our ability to scale-up data collection. Recent investigations have demonstrated that machine-learning approaches can facilitate this effort. However, present attempts have focused largely on simplistic binary coding of reproductive phenology (e.g., presence/absence of flowers). Here, we use crowd-sourced phenological data of buds, flowers, and fruits from >3,000 specimens of six common wildflower species of the eastern United States (Anemone canadensis L., A. hepatica L., A. quinquefolia L., Trillium erectum L., T. grandiflorum (Michx.) Salisb., and T. undulatum Wild.) to train models using Mask R-CNN to segment and count phenological features. A single global model was able to automate the binary coding of each of the three reproductive stages with >87% accuracy. We also successfully estimated the relative abundance of each reproductive structure on a specimen with ≥90% accuracy. Precise counting of features was also successful, but accuracy varied with phenological stage and taxon. Specifically, counting flowers was significantly less accurate than buds or fruits likely due to their morphological variability on pressed specimens. Moreover, our Mask R-CNN model provided more reliable data than non-expert crowd-sourcers but not botanical experts, highlighting the importance of high-quality human training data. Finally, we also demonstrated the transferability of our model to automated phenophase detection and counting of the three Trillium species, which have large and conspicuously-shaped reproductive organs. These results highlight the promise of our two-phase crowd-sourcing and machine-learning pipeline to segment and count reproductive features of herbarium specimens, thus providing high-quality data with which to investigate plant responses to ongoing climatic change.

Plastome phylogenomics, systematics, and divergence time estimation of the Beilschmiedia group (Lauraceae)

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 relatives. Our inferred phylogeny is robust and includes two major clades. The first includes a monophyletic Endiandra nested within a paraphyletic Australasian Beilschmiedia group. The second includes (i) a subclade of African Beilschmiedia plus Malagasy Potameia, (ii) a subclade of Asian species including Syndiclis and Sinopora, (iii) the lone Neotropical species B. immersinervis, (iv) a subclade of core Asian Beilschmiedia, sister to the Neotropical species B. brenesii, and v) two Asian species including B. turbinata and B. glauca. The rampant non-monophyly of Beilschmiedia we identify necessitates a major taxonomic realignment of the genus, including but not limited to the mergers of Brassiodendron and Sinopora into the genera Endiandra and Syndiclis, respectively. Along these lines, the high degree of continental, clade-wide endemism we identify suggests that geographical distribution may be a good proxy for delineating taxa within this group. Our molecular divergence time estimates indicate that stem Beilschmiedia group members date to the Early Eocene (~50 Ma); their crown age dates to the Eocene-Oligocene boundary (~34 Ma). These findings contradict older estimates of the group and support mounting evidence that the origin and diversification of many pantropical angiosperm clades are not easily attributed to strict western Gondwanan vicariance. Finally, our study highlights the phylogenetic utility of plastomes in Lauraceace, and lays a solid foundation for future phylogenomic and biogeographic investigations within the family.

Machine Learning Using Digitized Herbarium Specimens to Advance Phenological Research

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 growth and reproduction. As a major indicator of climate change, driver of ecological processes, and critical determinant of plant fitness, plant phenology is an important frontier for the application of ML techniques for science and society. In the present article, we describe a generalized, modular ML workflow for extracting phenological data from images of herbarium specimens, and we discuss the advantages, limitations, and potential future improvements of this workflow. Strategic research and investment in specimen-based ML methods, along with the aggregation of herbarium specimen data, may give rise to a better understanding of life on Earth.

Freezing and water availability structure the evolutionary diversity of trees across the Americas

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 predominant constraint in plant diversification and biogeography. We find a fundamental divide in tree lineage composition between tropical and extratropical environments, defined by the absence versus presence of freezing temperatures. Within the Neotropics, we uncover a further evolutionary split between moist and dry forests. Our results demonstrate that American tree lineages tend to retain their ancestral environmental relationships and that phylogenetic niche conservatism is the primary force structuring the distribution of tree biodiversity. Our study establishes the pervasive importance of niche conservatism to community assembly even at intercontinental scales.

Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution

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 two aquatic species-prickly waterlily (Euryale ferox; Nymphaeales) and the rigid hornwort (Ceratophyllum demersum; Ceratophyllales)-and expand the genomic representation for key sectors of the angiosperm tree of life. We identify multiple independent polyploidization events in each of the five major clades (that is, Nymphaeales, magnoliids, monocots, Ceratophyllales and eudicots). Furthermore, our phylogenomic analyses, which spanned multiple datasets and diverse methods, confirm that Amborella and Nymphaeales are successively sister to all other angiosperms. Furthermore, these genomes help to elucidate relationships among the major subclades within Mesangiospermae, which contain about 350,000 species. In particular, the species-poor lineage Ceratophyllales is supported as sister to eudicots, and monocots and magnoliids are placed as successively sister to Ceratophyllales and eudicots. Finally, our analyses indicate that incomplete lineage sorting may account for the incongruent phylogenetic placement of magnoliids between nuclear and plastid genomes.

Digitization and the Future of Natural History Collections

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. We broaden the current vision of digitization (Digitization 1.0)—whereby specimens are digitized within NHCs—to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds on the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data links, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical issues of global change.

Diverse trajectories of plastome degradation in holoparasitic Cistanche and genomic location of the lost plastid genes

The plastid genomes (plastomes) of non-photosynthetic plants generally undergo 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 sequence and assemble the complete plastomes of three holoparasitic Cistanche species (C. salsa, C. mongolica, and C. sinensis) and compare them with the available plastomes of Orobanchaceae. We identified that the diverse degradation trajectories under purifying selection existed among three Cistanche clades, showing obvious size differences in the entire plastome, long single copy region, and non-coding region, and different patterns of the retention/loss of functional genes. With few exceptions of putatively functional genes, massive plastid fragments, which have been lost and transferred into the mitochondrial or nuclear genomes, are non-functional. In contrast to the equivalents of the Orobanche species, some plastid-derived genes with diverse genomic locations are found in Cistanche. The early and initially diverged clades in different genera such as Cistanche and Aphyllon possess obvious patterns of plastome degradation, suggesting that such key lineages should be considered prior to comparative analysis of plastome evolution, especially in the same genus.

Evolution of Land Plants

The colonization of land by plants was one of the most important events in the earth’s history, setting the stage for the greening of the continents, increased oxygenation of the atmosphere, and the provision of food and habitat for the animals and microorganisms that evolved in parallel—and in many cases, diversified in their shadows. They are the foundation of agriculture and the source of timber, fibers, pharmaceuticals, and psychoactives. Fossilized plants, in particular, drive our global economy, being the source of coal, petroleum, and natural gas. And living plants represent huge above- and below-ground (as roots and microalgae) carbon sinks. Continental colonists who appeared before land plants (embryophytes) included prokaryotic microbes, eukaryotic microalgae, and fungi. The conditions necessary for colonization—sufficient areas of stable land accessible to marine and aquatic organisms, formation of soils, and equable atmospheric and climatic conditions—appear to have been established approximately 540–440 million years ago (ma; Cambrian and Ordovician). By about 470–460 ma (middle Ordovician), plant microfossils first appear in the fossil record, including spores, cuticular fragments, and tracheid cells. Early plant micro- and macrofossils, when considered together, displayed adaptations that facilitated survival on land, including coatings to reduce desiccation, stomata to facilitate gas exchange (in all lineages but liverworts), and specialized cells such as tracheids for the movement of water and nutrients (precursors of a vascular system). By about 410 ma (late Silurian to early Devonian), vegetation comprising small plants with a well-developed vascular system was establishing itself on multiple continents. From about 390–360 ma (middle to late Devonian), the number of species increased rapidly, and by 360 ma the major extant lineages of land plants were established. Major innovations in plant form began to appear, including the capacity to attain great height and size, and in the late Devonian period, the evolution of seeds. The seed provided protection during periods of dormancy and facilitated survival at greater distances from water. These events were followed during the Cretaceous/Cenozoic by one of the most spectacular radiations of any terrestrial clade: the rise of the angiosperms, which in the 21st century constitute about 90 percent of all land plant diversity.

Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval

Whole-genome duplications (WGDs) are widespread and prevalent in vascular plants and frequently coincide with major episodes of global and climatic upheaval, including the mass extinction at the Cretaceous-Tertiary boundary (c. 65 Ma) and during more recent periods of global aridification in the Miocene (c. 10-5 Ma). Here, we explore WGDs in the diverse flowering plant clade Malpighiales. Using transcriptomes and complete genomes from 42 species, we applied a multipronged phylogenomic pipeline to identify, locate, and determine the age of WGDs in Malpighiales using three means of inference: distributions of synonymous substitutions per synonymous site (Ks ) among paralogs, phylogenomic (gene tree) reconciliation, and a likelihood-based gene-count method. We conservatively identify 22 ancient WGDs, widely distributed across Malpighiales subclades. Importantly, these events are clustered around the Eocene-Paleocene transition (c. 54 Ma), during which time the planet was warmer and wetter than any period in the Cenozoic. These results establish that the Eocene Climatic Optimum likely represents a previously unrecognized period of prolific WGDs in plants, and lends further support to the hypothesis that polyploidization promotes adaptation and enhances plant survival during episodes of global change, especially for tropical organisms like Malpighiales, which have tight thermal tolerances.

Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta)

Gracilariaceae has a worldwide distribution including numerous economically important species. We applied high-throughput sequencing to obtain organellar genomes (mitochondria and chloroplast) from 10 species of Gracilariaceae and, combined with published genomes, to infer phylogenies and compare genome architecture among species representing main lineages. We obtained similar topologies between chloroplast and mitochondrial genomes phylogenies. However, the chloroplast phylogeny was better resolved with full support. In this phylogeny, Melanthalia intermedia is sister to a monophyletic clade including Gracilaria and Gracilariopsis, which were both resolved as monophyletic genera. Mitochondrial and chloroplast genomes were highly conserved in gene synteny, and variation mainly occurred in regions where insertions of plasmid-derived sequences (PDS) were found. In mitochondrial genomes, PDS insertions were observed in two regions where the transcription direction changes: between the genes cob and trnL, and trnA and trnN. In chloroplast genomes, PDS insertions were in different positions, but generally found between psdD and rrs genes. Gracilariaceae is a good model system to study the impact of PDS in genome evolution due to the frequent presence of these insertions in organellar genomes. Furthermore, the bacterial leuC/leuD operon was found in chloroplast genomes of Gracilaria tenuistipitata, G. chilensis, and M. intermedia, and in extrachromosomal plasmid of G. vermiculophylla. Phylogenetic trees show two different origins of leuC/leuD: genes found in chloroplast and plasmid were placed with proteobacteria, and genes encoded in the nucleus were close to Viridiplantae and cyanobacteria.

Biological collections for understanding biodiversity in the Anthropocene

Global change has become a central focus of modern biology. Yet, our knowledge of how anthropogenic drivers affect biodiversity and natural resources is limited by a lack of biological data spanning the Anthropocene. We propose that the hundreds of millions of plant, fungal and animal specimens deposited in natural history museums have the potential to transform the field of global change biology. We suggest that museum specimens are underused, particularly in ecological studies, given their capacity to reveal patterns that are not observable from other data sources. Increasingly, museum specimens are becoming mobilized online, providing unparalleled access to physiological, ecological and evolutionary data spanning decades and sometimes centuries. Here, we describe the diversity of collections data archived in museums and provide an overview of the diverse uses and applications of these data as discussed in the accompanying collection of papers within this theme issue. As these unparalleled resources are under threat owing to budget cuts and other institutional pressures, we aim to shed light on the unique discoveries that are possible in museums and, thus, the singular value of natural history collections in a period of rapid change.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

Herbarium specimens reveal substantial and unexpected variation in phenological sensitivity across the eastern United States

Phenology is a key biological trait that can determine an organism's survival and provides one of the clearest indicators of the effects of recent climatic change. Long time-series observations of plant phenology collected at continental scales could clarify latitudinal and regional patterns of plant responses and illuminate drivers of that variation, but few such datasets exist. Here, we use the web tool CrowdCurio to crowdsource phenological data from over 7000 herbarium specimens representing 30 diverse flowering plant species distributed across the eastern United States. Our results, spanning 120 years and generated from over 2000 crowdsourcers, illustrate numerous aspects of continental-scale plant reproductive phenology. First, they support prior studies that found plant reproductive phenology significantly advances in response to warming, especially for early-flowering species. Second, they reveal that fruiting in populations from warmer, lower latitudes is significantly more phenologically sensitive to temperature than that for populations from colder, higher-latitude regions. Last, we found that variation in phenological sensitivities to climate within species between regions was of similar magnitude to variation between species. Overall, our results suggest that phenological responses to anthropogenic climate change will be heterogeneous within communities and across regions, with large amounts of regional variability driven by local adaptation, phenotypic plasticity and differences in species assemblages. As millions of imaged herbarium specimens become available online, they will play an increasingly critical role in revealing large-scale patterns within assemblages and across continents that ultimately can improve forecasts of the impacts of climatic change on the structure and function of ecosystems.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

Digitization protocol for scoring reproductive phenology from herbarium specimens of seed plants

PREMISE OF THE STUDY

Herbarium specimens provide a robust record of historical plant phenology (the timing of seasonal events such as flowering or fruiting). However, the difficulty of aggregating phenological data from specimens arises from a lack of standardized scoring methods and definitions for phenological states across the collections community.

METHODS AND RESULTS

To address this problem, we report on a consensus reached by an iDigBio working group of curators, researchers, and data standards experts regarding an efficient scoring protocol and a data-sharing protocol for reproductive traits available from herbarium specimens of seed plants. The phenological data sets generated can be shared via Darwin Core Archives using the Extended MeasurementOrFact extension.

CONCLUSIONS

Our hope is that curators and others interested in collecting phenological trait data from specimens will use the recommendations presented here in current and future scoring efforts. New tools for scoring specimens are reviewed.

Widespread sampling biases in herbaria revealed from large-scale digitization

Nonrandom collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras online offer a timely opportunity to assess commonalities and differences in herbarium sampling biases. We determined spatial, temporal, trait, phylogenetic, and collector biases in c. 5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England, USA (NE). We identified numerous shared and unique biases among these regions. Shared biases included specimens collected close to roads and herbaria; specimens collected more frequently during biological spring and summer; specimens of threatened species collected less frequently; and specimens of close relatives collected in similar numbers. Regional differences included overrepresentation of graminoids in SA and AU and of annuals in AU; and peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by very few individuals. We hypothesize that these mega-collectors, with their associated preferences and idiosyncrasies, shaped patterns of collection bias via 'founder effects'. Studies using herbarium collections should account for sampling biases, and future collecting efforts should avoid compounding these biases to the extent possible.

Reading between the vines: Hosts as islands for extreme holoparasitic plants

PREMISE OF THE STUDY

Partitioning of population genetic variation in plants may be affected by numerous factors including life history and dispersal characteristics. In parasitic plants, interactions with host populations may be an additional factor influencing partitioning. To test for hierarchical population genetic patterns related to obligate endoparasitism, we studied three species of Rafflesiaceae, which grow as extremely reduced endophytes infecting Tetrastigma vines in Southeast Asia.

METHODS

Microsatellite markers were developed and multilocus genotypes were determined for Rafflesia cantleyi, Rafflesia tuan-mudae, and Sapria himalayana and each of their Tetrastigma hosts. Relatedness among parasite individuals was estimated, and AMOVAs were used to determine levels of population genetic subdivision.

KEY RESULTS

Microsatellite genotypes for 340 paired parasite and host samples revealed that host vines were infected by numerous Rafflesiaceae individuals that may spread for up to 14 m within stem tissues. Surprisingly, Rafflesiaceae parasites within a given host are significantly more closely related to each other than individuals of the same species in other host individuals. The pattern of hierarchical population genetic subdivision we detected across species is likely due to limited seed dispersal with reinfection of natal host vines.

CONCLUSIONS

These findings demonstrate common population genetic patterns between animal and plant parasites, potentially indicating advantages of close relatives infecting hosts. This study also has important conservation implications for Rafflesiaceae since our data suggest that destruction of a single infected host vine could result in large genetic losses.

CrowdCurio: an online crowdsourcing platform to facilitate climate change studies using herbarium specimens

Phenology is a key aspect of plant success. Recent research has demonstrated that herbarium specimens can provide important information on plant phenology. Massive digitization efforts have the potential to greatly expand herbarium-based phenological research, but also pose a serious challenge regarding efficient data collection. Here, we introduce CrowdCurio, a crowdsourcing tool for the collection of phenological data from herbarium specimens. We test its utility by having workers collect phenological data (number of flower buds, open flowers and fruits) from specimens of two common New England (USA) species: Chelidonium majus and Vaccinium angustifolium. We assess the reliability of using nonexpert workers (i.e. Amazon Mechanical Turk) against expert workers. We also use these data to estimate the phenological sensitivity to temperature for both species across multiple phenophases. We found no difference in the data quality of nonexperts and experts. Nonexperts, however, were a more efficient way of collecting more data at lower cost. We also found that phenological sensitivity varied across both species and phenophases. Our study demonstrates the utility of CrowdCurio as a crowdsourcing tool for the collection of phenological data from herbarium specimens. Furthermore, our results highlight the insight gained from collecting large amounts of phenological data to estimate multiple phenophases.

High-power lasers for directed-energy applications: reply

The comment by Vorontsov and Weyrauch [Appl. Opt.55, 9950 (2016)APOPAI0003-693510.1364/AO.55.009950] is aimed at rebutting the critiques in Sprangle et al. [Appl. Opt.54, F201 (2015)APOPAI0003-693510.1364/AO.54.00F201] and Nelson et al. [Appl. Opt.55, 1757 (2016)APOPAI0003-693510.1364/AO.55.001757]. In the comment, Vorontsov and colleagues describe their experiments aimed at demonstrating the feasibility of coherent combining of lasers on a distant target, using relatively low-power lasers and a cooperative retro-reflective target. The Naval Research Laboratory has demonstrated the capability to project high power on a distant target by making use of an incoherent combining architecture. The proof-of-concept experiments were performed in a realistic environment without employing cooperative targets and without sophisticated adaptive optics instrumentation.