Psychoactive and other ceremonial plants from a 2,000-year-old Maya ritual deposit at Yaxnohcah, Mexico

For millennia, healing and psychoactive plants have been part of the medicinal and ceremonial fabric of elaborate rituals and everyday religious practices throughout Mesoamerica. Despite the essential nature of these ritual practices to the societal framework of past cultures, a clear understanding of the ceremonial life of the ancient Maya remains stubbornly elusive. Here we record the discovery of a special ritual deposit, likely wrapped in a bundle, located beneath the end field of a Late Preclassic ballcourt in the Helena complex of the Maya city of Yaxnohcah. This discovery was made possible by the application of environmental DNA technology. Plants identified through this analytical process included Ipomoea corymbosa (xtabentun in Mayan), Capsicum sp. (chili pepper or ic in Mayan), Hampea trilobata (jool), and Oxandra lanceolata (chilcahuite). All four plants have recognized medicinal properties. Two of the plants, jool and chilcahuite, are involved in artifact manufacture that have ceremonial connections while chili peppers and xtabentun have been associated with divination rituals. Xtabentun (known to the Aztecs as ololiuhqui) produces highly efficacious hallucinogenic compounds and is reported here from Maya archaeological contexts for the first time.

Intra- and interspecific diversity in a tropical plant clade alter herbivory and ecosystem resilience

Declines in biodiversity generated by anthropogenic stressors at both species and population levels can alter emergent processes instrumental to ecosystem function and resilience. As such, understanding the role of biodiversity in ecosystem function and its response to climate perturbation is increasingly important, especially in tropical systems where responses to changes in biodiversity are less predictable and more challenging to assess experimentally. Using large-scale transplant experiments conducted at five neotropical sites, we documented the impacts of changes in intraspecific and interspecific plant richness in the genus Piper on insect herbivory, insect richness, and ecosystem resilience to perturbations in water availability. We found that reductions of both intraspecific and interspecific Piper diversity had measurable and site-specific effects on herbivory, herbivorous insect richness, and plant mortality. The responses of these ecosystem-relevant processes to reduced intraspecific Piper richness were often similar in magnitude to the effects of reduced interspecific richness. Increased water availability reduced herbivory by 4.2% overall, and the response of herbivorous insect richness and herbivory to water availability were altered by both intra- and interspecific richness in a site-dependent manner. Our results underscore the role of intraspecific and interspecific richness as foundations of ecosystem function and the importance of community and location-specific contingencies in controlling function in complex tropical systems.

Paleoecological Studies at the Ancient Maya Center of Yaxnohcah Using Analyses of Pollen, Environmental DNA, and Plant Macroremains

Yaxnohcah was a major city of the ancient Maya world, especially during the Preclassic period (1000 BCE–200 CE). Data from excavations provide important insights into the interactions between the ancient inhabitants and its surrounding Neotropical forests, a topic that, as a whole, remains largely enigmatic. This study aspired to fill that void in understanding by using traditional paleoethnobotanical approaches and a powerful new technology, the analysis of environmental DNA. Our results enabled us to characterize the vegetation growing in association with the principal structures and the artificial reservoirs that provided the city’s water supply. Because the area is without access to permanent water sources, such as rivers or lakes, these reservoirs were key to the development and survival of the city. Our results indicate that although there were large areas cleared for agricultural purposes, a mosaic of mature upland and bajo forest remained throughout the Maya occupation. In addition, our studies reveal that there were incursions of pine savanna into the area that may have been a reflection of prevailing edaphic conditions, or alternatively, the result of frequent burning.

The chemical ecology of tropical forest diversity: Environmental variation, chemical similarity, herbivory, and richness

Species richness in tropical forests is correlated with other dimensions of diversity, including the diversity of plant-herbivore interactions and the phytochemical diversity that influences those interactions. Understanding the complexity of plant chemistry and the importance of phytochemical diversity for plant-insect interactions and overall forest richness has been enhanced significantly by the application of metabolomics to natural systems. The present work used proton nuclear magnetic resonance spectroscopy (¹ H-NMR) profiling of crude leaf extracts to study phytochemical similarity and diversity among Piper plants growing naturally in the Atlantic Rainforest of Brazil. Spectral profile similarity and chemical diversity were quantified to examine the relationship between metrics of phytochemical diversity, specialist and generalist herbivory, and understory plant richness. Herbivory increased with understory species richness, while generalist herbivory increased and specialist herbivory decreased with the diversity of Piper leaf material available. Specialist herbivory increased when conspecific host plants were more spectroscopically dissimilar. Spectral similarity was lower among individuals of common species, and they were also more spectrally diverse, indicating phytochemical diversity is beneficial to plants. Canopy openness and soil nutrients also influenced chemistry and herbivory. The complex relationships uncovered in this study add information to our growing understanding of the importance of phytochemical diversity for plant-insect interactions and tropical plant species richness.

Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

Foundational hypotheses addressing plant-insect codiversification and plant defense theory typically assume a macroevolutionary pattern whereby closely related plants have similar chemical profiles. However, numerous studies have documented variation in the degree of phytochemical trait lability, raising the possibility that phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (1H NMR) data, chemical classification, and double digest restriction-site associated DNA sequencing (ddRADseq) to resolve evolutionary relationships and characterize the evolution of secondary chemistry in the Neotropical plant clade Radula (Piper; Piperaceae). Sequencing data substantially improved phylogenetic resolution relative to past studies, and spectroscopic characterization revealed the presence of 35 metabolite classes. Metabolite classes displayed phylogenetic signal, whereas the crude 1H NMR spectra featured little evidence of phylogenetic signal in multivariate tests of chemical resonances. Evolutionary correlations were detected in two pairs of compound classes (flavonoids with chalcones; p-alkenyl phenols with kavalactones), where the gain or loss of a class was dependent on the other's state. Overall, the evolution of secondary chemistry in Radula is characterized by strong phylogenetic signal of traditional compound classes and weak phylogenetic signal of specialized chemical motifs, consistent with both classic evolutionary hypotheses and recent examinations of phytochemical evolution in young lineages.

Environmental DNA reveals arboreal cityscapes at the Ancient Maya Center of Tikal

Tikal, a major city of the ancient Maya world, has been the focus of archaeological research for over a century, yet the interactions between the Maya and the surrounding Neotropical forests remain largely enigmatic. This study aimed to help fill that void by using a powerful new technology, environmental DNA analysis, that enabled us to characterize the site core vegetation growing in association with the artificial reservoirs that provided the city water supply. Because the area has no permanent water sources, such as lakes or rivers, these reservoirs were key to the survival of the city, especially during the population expansion of the Classic period (250-850 CE). In the absence of specific evidence, the nature of the vegetation surrounding the reservoirs has been the subject of scientific hypotheses and artistic renderings for decades. To address these hypotheses we captured homologous sequences of vascular plant DNA extracted from reservoir sediments by using a targeted enrichment approach involving 120-bp genetic probes. Our samples encompassed the time before, during and after the occupation of Tikal (1000 BCE-900 CE). Results indicate that the banks of the ancient reservoirs were primarily fringed with native tropical forest vegetation rather than domesticated species during the Maya occupation.

Chemical and Genotypic Variations in Aniba rosiodora from the Brazilian Amazon Forest

Aniba rosiodora has been exploited since the end of the nineteenth century for its essential oil, a valuable ingredient in the perfumery industry. This species occurs mainly in Northern South America, and the morphological similarity among different Aniba species often leads to misidentification, which impacts the consistency of products obtained from these plants. Hence, we compared the profiles of volatile organic compounds (essential oils) and non-volatile organic compounds (methanolic extracts) of two populations of A. rosiodora from the RESEX and FLONA conservation units, which are separated by the Tapajós River in Western Pará State. The phytochemical profile indicated a substantial difference between the two populations: samples from RESEX present α-phellandrene (22.8%) and linalool (39.6%) in their essential oil composition, while samples from FLONA contain mainly linalool (83.7%). The comparison between phytochemical profiles and phylogenetic data indicates a clear difference, implying genetic distinction between these populations.

Evaluation of DNA markers for molecular identification of three Piper species from Brazilian Atlantic Rainforest

Piper is one of two large genera in the Piperaceae, and with ca. 2600 species, is one of the largest plant genera in the world. Species delimitation and evaluation of genetic diversity among populations are important requisites for conservation and adequate exploitation of economically important species. DNA barcoding has been used as a powerful tool and a practical method for species characterization and delimitation. The present work aims to evaluate molecular markers for barcoding three Piper species native to Brazil: P. gaudichaudianum (“jaborandi” or “pariparoba”), P. malacophyllum (“pariparoba-murta”) and P. regnellii (“caapeba” or “pariparoba”). A reference DNA barcode library was developed using sequences of three candidate regions: ITS2, trnH-psbA and rbcL. Transferability of the microsatellite (SSR) primers Psol 3, Psol 6 and Psol 10, designed originally for Piper solmsianum, to the three Piper species was also evaluated. The discriminatory power of the markers was based on the determination of inter- and intraspecific distances, phylogenetic reconstruction, and clustering analysis, as well as BLASTn comparison. Sequences of ITS2 enabled efficient species identification by means of the BLASTn procedure. Based on these sequences, intraspecific divergence was lower than interspecific variation. Maximum Parsimony analyses based on ITS2 sequences provided three resolved clades, each corresponding to one of the three analysed species. Sequences of trnH-psbA and rbcL had lower discriminatory value. Analyses combining sequences of these regions were less effective toward the attainment of resolved and strongly supported clades of all species. In summary, robustly supported clades of P. regnellii were obtained in most of the analyses, based either on isolated or combined sequences. The SSRs primers Psol 3, Psol 6 and Psol 10 were shown to be transferable to P. gaudichaudianum and P. regnellii, but not to P. malacophyllum. Preliminary cluster analyses based on the polymorphism of the amplified products suggested that Psol 3 has lower potential than Psol 6 and Psol 10 for discrimination of Piper species.

Molecular genetic and geochemical assays reveal severe contamination of drinking water reservoirs at the ancient Maya city of Tikal

Understanding civilizations of the past and how they emerge and eventually falter is a primary research focus of archaeological investigations because these provocative data sets offer critical insights into long-term human behavior patterns, especially in regard to land use practices and sustainable environmental interactions. The ancient Maya serve as an intriguing example of this research focus, yet the details of their spectacular emergence in a tropical forest environment followed by their eventual demise have remained enigmatic. Tikal, one of the foremost of the ancient Maya cities, plays a central role in this discussion because of its sharp population decline followed by abandonment during the late 9th century CE. Our results, based on geochemical and molecular genetic assays on sediments from four of the main reservoirs, reveal that two of the largest reservoirs at Tikal, essential for the survival of the city during the dry seasons, were contaminated with high levels of mercury, phosphate and cyanobacteria known to produce deadly toxins. Our observations demonstrate severe pollution problems at a time when episodes of climatic aridity were prevalent. This combination of catastrophic events clearly threatened the sustainability of the city and likely contributed to its abandonment.

A series of unfortunate events: the forgotten botanist and the misattribution of a type collection

In 1777, Spain sent The Royal Expedition to Peru and Chile, commonly referred to as the "Ruiz and Pavón Expedition", to document the flora of this richly diverse part of its colonies. The Expedition was active in the New World for 38 years and was led by Hipólito Ruiz and José Pavón, who collected in Peru and Chile for the first 11 years before returning to Spain to work on publication of the Flora Peruviana, et Chilensis. Work on the ground for the reminder of the project in Peru and later Ecuador, was continued by Juan Tafalla and Juan Manzanilla. With few exceptions, all collections from the Expedition including types, have conventionally been attributed to Ruiz and Pavón despite the fact that Tafalla and Manzanilla were responsible for a large part of the collections. The purpose of this note is to bring to light the important but often overlooked figure of Juan Tafalla, to highlight his accomplishments as a collector and to increase precision in botanical nomenclature by giving him due credit by correctly attributing collections.

Intraspecific phytochemical variation shapes community and population structure for specialist caterpillars

Chemically mediated plant-herbivore interactions contribute to the diversity of terrestrial communities and the diversification of plants and insects. While our understanding of the processes affecting community structure and evolutionary diversification has grown, few studies have investigated how trait variation shapes genetic and species diversity simultaneously in a tropical ecosystem. We investigated secondary metabolite variation among subpopulations of a single plant species, Piper kelleyi (Piperaceae), using high-performance liquid chromatography (HPLC), to understand associations between plant phytochemistry and host-specialized caterpillars in the genus Eois (Geometridae: Larentiinae) and associated parasitoid wasps and flies. In addition, we used a genotyping-by-sequencing approach to examine the genetic structure of one abundant caterpillar species, Eois encina, in relation to host phytochemical variation. We found substantive concentration differences among three major secondary metabolites, and these differences in chemistry predicted caterpillar and parasitoid community structure among host plant populations. Furthermore, E. encina populations located at high elevations were genetically different from other populations. They fed on plants containing high concentrations of prenylated benzoic acid. Thus, phytochemistry potentially shapes caterpillar and wasp community composition and geographic variation in species interactions, both of which can contribute to diversification of plants and insects.

Host conservatism, host shifts and diversification across three trophic levels in two Neotropical forests

Host-parasite systems have been models for understanding the connection between shifts in resource use and diversification. Despite theoretical expectations, ambiguity remains regarding the frequency and importance of host switches as drivers of speciation in herbivorous insects and their parasitoids. We examine phylogenetic patterns with multiple genetic markers across three trophic levels using a diverse lineage of geometrid moths (Eois), specialist braconid parasitoids (Parapanteles) and plants in the genus Piper. Host-parasite associations are mapped onto phylogenies, and levels of cospeciation are assessed. We find nonrandom patterns of host use within both the moth and wasp phylogenies. The moth-plant associations in particular are characterized by small radiations of moths associated with unique host plants in the same geographic area (i.e. closely related moths using the same host plant species). We suggest a model of diversification that emphasizes an interplay of factors including host shifts, vicariance and adaptation to intraspecific variation within hosts.

A new species of Solanum named for Jeanne Baret, an overlooked contributor to the history of botany

We describe Solanum baretiaesp. nov., a new species of Solanum section Anarrhichomenum, named in honor of Jeanne Baret, who sailed as the assistant to botanist Philibert Commerson on Louis Antoine de Bougainville's global circumnavigation (1766-1769). The species is similar to Solanum chimborazense, but differs in having larger flowers, more flowers per inflorescence, and different patterns of pubescence on the filaments (pubescent adaxially and glabrous abaxially) and style (papillose to sparsely pubescent). A description, illustration, photos, and comparisons to similar species are included. Also included is a preliminary conservation assessment, along with a brief account of the important role played by Baret during the expedition. The new species appears to be restricted to the Amotape-Huancabamba zone, an area of southern Ecuador and northern Peru known for its exceptional biodiversity.

Multiple recent horizontal transfers of the cox1 intron in Solanaceae and extended co-conversion of flanking exons

Background

The most frequent case of horizontal transfer in plants involves a group I intron in the mitochondrial gene cox1, which has been acquired via some 80 separate plant-to-plant transfer events among 833 diverse angiosperms examined. This homing intron encodes an endonuclease thought to promote the intron's promiscuous behavior. A promising experimental approach to study endonuclease activity and intron transmission involves somatic cell hybridization, which in plants leads to mitochondrial fusion and genome recombination. However, the cox1 intron has not yet been found in the ideal group for plant somatic genetics - the Solanaceae. We therefore undertook an extensive survey of this family to find members with the intron and to learn more about the evolutionary history of this exceptionally mobile genetic element.

Results

Although 409 of the 426 species of Solanaceae examined lack the cox1 intron, it is uniformly present in three phylogenetically disjunct clades. Despite strong overall incongruence of cox1 intron phylogeny with angiosperm phylogeny, two of these clades possess nearly identical intron sequences and are monophyletic in intron phylogeny. These two clades, and possibly the third also, contain a co-conversion tract (CCT) downstream of the intron that is extended relative to all previously recognized CCTs in angiosperm cox1. Re-examination of all published cox1 genes uncovered additional cases of extended co-conversion and identified a rare case of putative intron loss, accompanied by full retention of the CCT.

Conclusions

We infer that the cox1 intron was separately and recently acquired by at least three different lineages of Solanaceae. The striking identity of the intron and CCT from two of these lineages suggests that one of these three intron captures may have occurred by a within-family transfer event. This is consistent with previous evidence that horizontal transfer in plants is biased towards phylogenetically local events. The discovery of extended co-conversion suggests that other cox1 conversions may be longer than realized but obscured by the exceptional conservation of plant mitochondrial sequences. Our findings provide further support for the rampant-transfer model of cox1 intron evolution and recommend the Solanaceae as a model system for the experimental analysis of cox1 intron transfer in plants.

A 10-gene phylogeny of Solanum section Herpystichum (Solanaceae) and a comparison of phylogenetic methods

PREMISE OF THE STUDY

Solanum section Herpystichum is a lineage that comprises both widespread and very narrowly distributed species. This study investigates the phylogenetic relationships of sect. Herpystichum and evaluates several phylogenetic methods for analysis of multiple sequences.

METHODS

Sequence data from seven nuclear (ITS, GBSSI, and five COSII) and three plastid (psbA-trnH, trnT-trnF, and trnS-trnG) regions were concatenated and analyzed under maximum parsimony and Bayesian criteria. In addition, we used two analytical methods that take into account differences in topologies resulting from the analyses of the individual markers: Bayesian Estimation of Species Trees (BEST) and supertree analysis.

KEY RESULTS

The monophyletic Solanum sect. Herpystichum was resolved with moderate support in the concatenated maximum parsimony and Bayesian analyses and the supertree analysis, and relationships within the section were well-resolved and strongly supported. The BEST topology, however, was poorly resolved. Also, because of how BEST deals with missing sequences, >25% of our accessions, including two species, had to be excluded from the analyses. Our results indicate a progenitor-descendent relationship with two species nested within the widespread S. evolvulifolium.

CONCLUSIONS

Analytical methods that consider individual topologies are important for studies based on multiple molecular markers. On the basis of analyses in this study, BEST had the serious shortcoming that taxa with missing sequences must be removed from the analysis or they can produce spurious topologies. Supertree analysis provided a good alternative for our data by allowing the inclusion of all 10 species of sect. Herpystichum.

Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies

One of the longstanding questions in phylogenetic systematics is how to address incongruence among phylogenies obtained from multiple markers and how to determine the causes. This study presents a detailed analysis of incongruent patterns between plastid and ITS/ETS phylogenies of Tribe Senecioneae (Asteraceae). This approach revealed widespread and strongly supported incongruence, which complicates conclusions about evolutionary relationships at all taxonomic levels. The patterns of incongruence that were resolved suggest that incomplete lineage sorting (ILS) and/or ancient hybridization are the most likely explanations. These phenomena are, however, extremely difficult to distinguish because they may result in similar phylogenetic patterns. We present a novel approach to evaluate whether ILS can be excluded as an explanation for incongruent patterns. This coalescence-based method uses molecular dating estimates of the duration of the putative ILS events to determine if invoking ILS as an explanation for incongruence would require unrealistically high effective population sizes. For four of the incongruent patterns identified within the Senecioneae, this approach indicates that ILS cannot be invoked to explain the observed incongruence. Alternatively, these patterns are more realistically explained by ancient hybridization events.

Characterizing the cauline domatia of two newly discovered ecuadorian ant plants in piper: an example of convergent evolution

The stems of some myrmecophytes in Piper are used as domatia by resident ant colonies. Hollow, ant-occupied stems were previously known only in four species of southern Central American Piper, all members of Section Macrostachys. Here we present two additional, unrelated, hollow-stemmed myrmecophytes from Ecuador: P. immutatum and P. pterocladum (members of sections Radula and Peltobryon, respectively). Although similar superficially, stem cavities of the Ecuadorian Piper species differ morphologically and developmentally from those of Central American taxa. The stem cavities of P. immutatum, and possibly P. pterocladum, are formed during stem development, and begin forming only a few millimeters behind the apical meristem. This mode of cavity formation differs markedly from myrmecophytes in section Macrostachys, where the stems remain solid unless excavated by the specialized ant partner Pheidole bicornis. The stems of P. immutatum and P. pterocladum do not produce wound-response tissue around the cavity, unlike the stems in section Macrostachys. The entrance holes in stems of P. immutatum are formed through apoptotic processes and are located at each node below the petiole, whereas those in section Macrostachys are excavated by the ants in the leaf axil. This study documents convergent evolution of ant-plant associations in Piper, and emphasizes the need for careful comparison of apparently homologous, ant-associated structures in specialized myrmecophytes.

Stem diversity, cauline domatia, and the evolution of ant-plant associations in Piper sect. Macrostachys (Piperaceae)

Plants possess a variety of structures that harbor ant nests, and the morphology of these domatia determines the nature of ant-plant mutualisms in a given plant species. In this study, we report on the differences in anatomy between myrmecophytes of Piper, which are regularly excavated by an obligate ant mutualist (Pheidole bicornis) and nonmyrmecophytes of Piper, which consistently have solid stems. Stems of excavated plant species lacked outward evidence of modification; however, striking anatomical differences were apparent between hollow-stemmed species before excavation and the remainder of the solid-stemmed species studied. Prior to excavation by ants, stems of myrmecophytes were characterized by strongly heterogeneous piths in which a large, central area had relatively large cells lacking intracellular crystals with a periphery of smaller cells containing numerous crystals. The domatium excavated by the ants was restricted to the large-celled region. This is the first report of the absence of crystals in ant-excavated portions of stems of myrmecophytes. Cauline domatia became lined with 3-8 cell layers of suberized wound tissue, which may have an impact on nutrient absorption by Piper myrmecophytes.