Integrating datasets from herbarium specimens and images to treat a Neotropical myrtle species complex.

BACKGROUND AND AIMS: Herbaria are the most important source of information for plant taxonomic work. Resources and technologies available today, such as digitised collections and herbarium DNA sequencing, can help accelerate taxonomic decisions in challenging plant groups. Here we employ an integrative methodology relying exclusively on herbarium specimens to investigate species boundaries in the Neotropical Myrcia neoobscura complex (Myrtaceae). METHODS: We collected morphometric data from high-resolution images of herbarium sheets and analysed it using hierarchical clustering. We posteriorly tested the obtained morpho-groups with phylogenomics using the Angiosperms353 probe kit. We also gathered phenological and geographic information from specimen labels and built phenological histograms and ecological niche models to investigate ecological differences amongst taxa. KEY RESULTS: Current circumscriptions of Myrcia arenaria, Myrcia neoglabra and Myrcia neoregeliana are confirmed in this study. Conversely, the four pieces of evidence together support Calyptranthes langsdorffii var. grandiflora, Marlierea regeliana var. parviflora and Marlierea warmingiana as separate from Myrcia marliereana, Myrcia neoriedeliana and Myrcia neoobscura, respectively, contrary to arrangements proposed by previous authors. Integrated analyses also support separation between Myrcia excoriata and two similar, undescribed taxa. CONCLUSIONS: Our data reveal the need for major changes in the systematics of the group, with recognition of 12 species. The successful delivery of our study aims was possible due to obtaining robust, high-quality data from museum specimens. We emphasise the importance of maintaining botanical collections physically and digitally available for taxonomic work and advocate their use to accelerate holistic taxonomic solutions of tropical species complexes. This is urgent, given the paucity of funds for fieldwork and unprecedented rates of habitat loss in the tropics.

Towards a species-level phylogeny for Neotropical Myrtaceae: Notes on topology and resources for future studies.

PREMISE: Increasingly complete phylogenies underpin studies in systematics, ecology, and evolution. Myrteae (Myrtaceae), with ~2700 species, is a key component of the exceptionally diverse Neotropical flora, but given its complicated taxonomy, automated assembling of molecular supermatrices from public databases often lead to unreliable topologies due to poor species identification. METHODS: Here, we build a taxonomically verified molecular supermatrix of Neotropical Myrteae by assembling 3909 published and 1004 unpublished sequences from two nuclear and seven plastid molecular markers. We infer a time-calibrated phylogenetic tree that covers 712 species of Myrteae (~28% of the total diversity in the clade) and evaluate geographic and taxonomic gaps in sampling. RESULTS: The tree inferred from the fully concatenated matrix mostly reflects the topology of the plastid data set and there is a moderate to strong incongruence between trees inferred from nuclear and plastid partitions. Large, species-rich genera are still the poorest sampled within the group. Eastern South America is the best-represented area in proportion to its species diversity, while Western Amazon, Mesoamerica, and the Caribbean are the least represented. CONCLUSIONS: We provide a time-calibrated tree that can be more reliably used to address finer-scale eco-evolutionary questions that involve this group in the Neotropics. Gaps to be filled by future studies include improving representation of taxa and areas that remain poorly sampled, investigating causes of conflict between nuclear and plastid partitions, and the role of hybridization and incomplete lineage sorting in relationships that are poorly supported.

Evidence-based guidelines for automated conservation assessments of plant species.

Assessing species' extinction risk is vital to setting conservation priorities. However, assessment endeavors, such as those used to produce the IUCN Red List of Threatened Species, have significant gaps in taxonomic coverage. Automated assessment (AA) methods are gaining popularity to fill these gaps. Choices made in developing, using, and reporting results of AA methods could hinder their successful adoption or lead to poor allocation of conservation resources. We explored how choice of data cleaning type and level, taxonomic group, training sample, and automation method affect performance of threat status predictions for plant species. We used occurrences from the Global Biodiversity Information Facility (GBIF) to generate assessments for species in 3 taxonomic groups based on 6 different occurrence-based AA methods. We measured each method's performance and coverage following increasingly stringent occurrence cleaning. Automatically cleaned data from GBIF performed comparably to occurrence records cleaned manually by experts. However, all types of data cleaning limited the coverage of AAs. Overall, machine-learning-based methods performed well across taxa, even with minimal data cleaning. Results suggest a machine-learning-based method applied to minimally cleaned data offers the best compromise between performance and species coverage. However, optimal data cleaning, training sample, and automation methods depend on the study group, intended applications, and expertise.

La valoración del riesgo de extinción de las especies es vital para el establecimiento de prioridades de conservación. Sin embargo, los esfuerzos de valoración, como los que se usan para generar la Lista Roja de Especies Amenazadas de la UICN, tienen brechas importantes en la cobertura taxonómica. Los métodos de valoración automatizada (VA) están ganando popularidad como reductores de estas brechas. Las elecciones realizadas en el desarrollo, uso y reporte de resultados de los métodos de VA podrían obstaculizar su adopción exitosa o derivar en una asignación deficiente de recursos para la conservación. Exploramos cómo la selección del tipo de limpieza de datos y el nivel, grupo taxonómico, muestra de entrenamiento y el método de automatización afectan el desempeño de las predicciones del estado de amenaza de las especies de plantas. Usamos los registros de la Global Biodiversity Information Facility (GBIF) para generar las valoraciones de las especies de tres grupos taxonómicos con base en seis métodos diferentes de VA basados en la presencia de las especies. Medimos el desempeño de cada método y cobertura después de una limpieza de presencia cada vez más estricta. La información de la GBIF limpiada automáticamente tuvo un desempeño comparable con los registros de presencia limpiados manualmente por expertos. Sin embargo, todos los tipos de limpieza de datos limitaron la cobertura de las valoraciones automatizadas. En general, los métodos basados en el aprendizaje automático tuvieron un buen desempeño en todos los taxones, incluso con una limpieza mínima de datos. Los resultados sugieren que un método basado en el aprendizaje automático aplicado a información con la mínima limpieza ofrece el mejor equilibrio entre el desempeño y la cobertura de la especie. A pesar de esto, la limpieza óptima de datos, la muestra de entrenamiento y los métodos de automatización dependen del grupo de estudio, las aplicaciones deseadas y la experiencia.

Diversity, phylogeny and evolution of the rapidly evolving genus Psidium L. (Myrtaceae, Myrteae).

BACKGROUND AND AIMS: Psidium is the fourthth largest genus of Myrtaceae in the Neotropics. Psidium guajava is widely cultivated in the tropics for its edible fruit. It is commercially under threat due to the disease guava decline. Psidium cattleyanum is one of the 100 most invasive organisms in the world. Knowledge of the phylogenetic relationships within Psidium is poor. We aim to provide a review of the biology, morphology and ecology of Psidium, a phylogenetic tree, an infrageneric classification and a list of species. METHODS: Morphological and geographic data were obtained by studying Psidium in herbaria and in the field between 1988 and 2020. Forty-six herbaria were visited personally. A database of approx. 6000 specimens was constructed, and the literature was reviewed. Thirty species (about a third of the species in the genus) were sampled for molecular phylogenetic inference. Two chloroplast (psbA-trnH and ndhF) and two nuclear (external transcribed spacer and internal transcribed spacer) regions were targeted. Phylogenetic trees were constructed using maximum likelihood (ML; RaxML) and Bayesian inference (BI; MrBayes). KEY RESULTS: Psidium is a monophyletic genus with four major clades recognized as sections. Section Psidium (ten species), to which P. guajava belongs, is sister to the rest of the genus; it is widespread across the Neotropics. Section Obversifolia (six species; restricted to the Brazilian Atlantic Forest), which includes P. cattleyanum, is sister to the innermost clade composed of sister sections Apertiflora (31 species; widespread but most diverse in the Brazilian Atlantic Forest) + Mitranthes (26 species; widespread in dry forests and probably diverse in the Caribbean). Characters associated with diversification within Psidium are discussed. CONCLUSIONS: Research on pre-foliation, colleters, leaf anatomy, leaf physiology, staminal development, placentation and germination associated with the anatomy of the opercular plug is desirable. Studies are biased towards sections Psidium and Obversifolia, with other sections poorly known.

Phylogeny and biogeography of Myrcia sect. Aguava (Myrtaceae, Myrteae) based on phylogenomic and Sanger data provide evidence for a Cerrado origin and geographically structured clades.

Myrcia is one of the largest exclusively Neotropical angiosperm genera, including ca. 800 species divided into nine sections. Myrcia sect. Aguava is one of most complex sections of Myrcia due to high morphological variation and wide distribution range of some species, including M. guianensis, with distribution throughout South America and a complex taxonomic history. We used complete plastid DNA sequences data generated using next-generation sequencing of 45 terminals, mostly from Myrcia sect. Aguava. These data were combined with five target DNA regions (ITS, psbA-trnH, trnL-trnF, trnQ-rps16, ndhF) of additional terminals to increase taxonomic coverage. Phylogenetic analyses were conducted using a maximum likelihood approach, and divergence times and ancestral range distributions were estimated. Myrcia sect. Aguava is monophyletic and exclusively comprises species with trilocular ovaries but has no relationship with other groups within Myrcia that possess trilocular ovaries. Three main lineages that correspond to geographical distribution are recognized within Myrcia sect. Aguava. Multiple accessions reveal a non-monophyletic Myrcia guianensis and stress the biogeographical structure inside the group. Myrcia sect. Aguava had a probable mid-Miocene origin in the Cerrado, but lineages that persisted there diversified only more recently, when the present-day vegetation started to stabilize. Posterior migrations to Atlantic Forest, Amazon and Caribbean occurred at the end of Miocene, evidencing transitions from open and dry to forested and more humid areas that are less frequent in the Neotropics. Overall, it is observed that related lineages remained in ecologically similar environments. Future perspectives on Myrcia and Myrteae in the phylogenomic era are also discussed.

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set.

PREMISE: To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS: We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS: Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. CONCLUSIONS: High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

Floral uniformity through evolutionary time in a species-rich tree lineage.

Changes in floral morphology are expected across evolutionary time and are often promoted as important drivers in angiosperm diversification. Such a statement, however, is in contrast to empirical observations of species-rich lineages that show apparent conservative floral morphologies even under strong selective pressure to change from their environments. Here, we provide quantitative evidence for prolific speciation despite uniform floral morphology in a tropical species-rich tree lineage. We analyse floral disparity in the environmental and phylogenetic context of Myrcia (Myrtaceae), one of the most diverse and abundant tree genera in Neotropical biomes. Variation in floral morphology among Myrcia clades is exceptionally low, even among distantly related species. Discrete floral specialisations do occur, but these are few, present low phylogenetic signal, have no strong correlation with abiotic factors, and do not affect overall macroevolutionary dynamics in the lineage. Results show that floral form and function may be conserved over large evolutionary time scales even in environments full of opportunities for ecological interactions and niche specialisation. Species accumulation in diverse lineages with uniform flowers apparently does not result from shifts in pollination strategies, but from speciation mechanisms that involve other, nonfloral plant traits.

Advanced understanding of phylogenetic relationships, morphological evolution and biogeographic history of the mega-diverse plant genus Myrcia and its relatives (Myrtaceae: Myrteae).

Myrcia is the largest exclusively Neotropical genus of the plant family Myrtaceae with c. 770 species. Although several studies have elucidated the relationships within particular sections of the genus, to date no phylogeny has been produced that includes a broad taxonomic and geographic representation. Here we present a phylogenetic hypothesis of Myrcia and close relatives comprising 253 species and based on two nuclear and seven plastid markers. We combine previously available sequence data with 234 new sequences of the genus Myrcia for this study. We use this phylogeny to investigate the evolution of selected morphological traits and to infer the biogeographic history of the genus. Our results yield a highly supported phylogenetic tree where the Myrceugenia group is sister to the Myrcia and Plinia groups. Five Myrcia species previously considered unplaced emerge in a newly circumscribed clade. The monophyly of two Myrcia sections previously considered uncertain, Aulomyrcia and Gomidesia, are confirmed with strong support. Flowers with free calyx lobes, 2-locular ovaries, and anthers with symmetrical thecae are ancestral features of Myrcia. The Myrcia sect. Gomidesia is highly supported and recovered as monophyletic, with asymmetric anthers that retain their curvature after dehiscence as a morphological synapomorphy. The Atlantic Forest is the most likely ancestral area of the genus and most of its internal clades, from where multiple lineages colonized different regions of South and Central America, in particular the Brazilian Cerrado through multiple unidirectional range expansions. The southern Atlantic Forest is the ancestral area for Myrcia sect. Gomidesia, with lineages reaching the northern Atlantic Forest, Cerrado, Yungas, and other savanna vegetation of South America. Our results provide a solid backbone for further evolutionary and taxonomic work and clarify several previously uncertain relationships in this mega-diverse plant group, and shed light on its geographical range evolution.

Calyx (con)fusion in a hyper-diverse genus: Parallel evolution of unusual flower patterns in Eugenia (Myrtaceae).

Eugenia has a pantropical distribution and comprises ca. 1000 species found mostly in the Neotropics. Recent DNA based phylogenies show that unusual flower morphology of 'eugenioid' collections, e.g. fused calices that open by tearing, consistently emerged within Eugenia. These results emphasize a demand to revaluate flower morphology in a phylogenetic context within the genus. A reassessment of calyx fusion in Eugenia and traditionally related genera is here focused on clarification of the systematic relevance of this apparently recurrent characteristic. Twenty-four Eugenia species with some level of calyx fusion in the bud were newly used (one nuclear and four plastid markers) in conjunction with a representative sample of previously sequenced species to recover a time-calibrated Eugenia phylogeny of 86 accessions. Development of the fused calyx was analysed using scanning electron microscopy, differing patterns were re-coded and subsequently phylogenetic character reconstruction was performed. Eugenia was recovered as monophyletic including the traditionally segregated genera Calycorectes and Catinga. Ancestral character reconstruction uncovered free calyx lobes as the ancestral condition. Five development patterns leading to calyx fusion are reported in Eugenia including species with apparently six petals, which contrast with the standard tetramerous flowers. This condition is interpreted as the petaloid pattern, where two external fused calyx lobes cover the bud while two internal calyx lobes are free and petaloid. The fused calyx condition is homoplastic and evolved independently, several times in Eugenia, as did the different development patterns. Data presented here show that systematic incongruence resulting from multiple, independent origins of the fused calyx in Eugenia is further aggravated by an inability to distinguish parallelism and convergence within the recovered patterns.

Harnessing the potential of integrated systematics for conservation of taxonomically complex, megadiverse plant groups.

The value of natural history collections for conservation science research is increasingly recognized, despite their well-documented limitations in terms of taxonomic, geographic, and temporal coverage. Specimen-based analyses are particularly important for tropical plant groups for which field observations are scarce and potentially unreliable due to high levels of diversity-amplifying identification challenges. Specimen databases curated by specialists are rich sources of authoritatively identified, georeferenced occurrence data, and such data are urgently needed for large genera. We compared entries in a monographic database for the large Neotropical genus Myrcia in 2007 and 2017. We classified and quantified differences in specimen records over this decade and determined the potential impact of these changes on conservation assessments. We distinguished misidentifications from changes due to taxonomic remodeling and considered the effects of adding specimens and georeferences. We calculated the potential impact of each change on estimates of extent of occurrence (EOO), the most frequently used metric in extinction-risk assessments of tropical plants. We examined whether particular specimen changes were associated with species for which changes in EOO over the decade were large enough to change their conservation category. Corrections to specimens previously misidentified or lacking georeferences were overrepresented in such species, whereas changes associated with taxonomic remodeling (lumping and splitting) were underrepresented. Among species present in both years, transitions to less threatened status outnumbered those to more threatened (8% vs 3%, respectively). Species previously deemed data deficient transitioned to threatened status more often than to not threatened (10% vs 7%, respectively). Conservation scientists risk reaching unreliable conclusions if they use specimen databases that are not actively curated to reflect changing knowledge.

Empleo del Potencial de la Sistemática Integrada para la Conservación de Grupos Botánicos Complejos y Megadiversos Resumen Cada vez se reconoce más el valor que tienen las colecciones de historia natural para la investigación dentro de la ciencia de la conservación, a pesar de las limitaciones en la documentación adecuada de la cobertura taxonómica, geográfica y temporal. Los análisis con base en especímenes son de particular importancia en los grupos de plantas tropicales, para los cuales las observaciones en el campo son escasas y potencialmente de poca confianza debido la gran cantidad de retos de identificación que amplifican la diversidad. Las bases de datos de especímenes que son curadas por especialistas son fuentes abundantes de datos identificados autoritativamente y de distribución georeferenciada, por lo que es urgente la necesidad de dichos datos para géneros extensos. Comparamos las entradas en una base de datos monográfica para el género neotropical extenso Myrcia en 2007 y en 2017. Clasificamos y cuantificamos las diferencias en los registros de especímenes durante esta década y determinamos el impacto potencial de estos cambios sobre las evaluaciones de conservación. Separamos las identificaciones erróneas de los cambios causados por la remodelación taxonómica y consideramos los efectos de la adición de especímenes y de georeferencias. Calculamos el impacto potencial de cada cambio sobre las estimaciones de la extensión de la distribución (EOO, en inglés), la medida que se utiliza con mayor frecuencia en las valoraciones del riesgo de extinción de las plantas tropicales. Examinamos si los cambios en un espécimen particular estuvieron asociados con especies para las cuales los cambios en la EOO durante la década fueron lo suficientemente amplios para cambiarles la categoría de conservación. Las correcciones hechas a especímenes previamente mal identificados o carentes de georeferencias estuvieron sobre-representadas en dichas especies, mientras que los cambios asociados con la remodelación taxonómica (agrupamiento y separación) estuvieron sub-representados. Entre las especies presentes en ambos años, las transiciones hacia un estado de conservación con menor amenaza superaron en cantidad a aquellas hacia un estado de mayor amenaza (8% vs 3%, respectivamente). Las especies que con anterioridad se clasificaban como deficientes de datos tuvieron más transiciones hacia el estado de amenazadas que hacia el estado de no amenazadas (10% vs 7%, respectivamente). Los científicos de la conservación corren el riesgo de llegar a conclusiones poco confiables si utilizan bases de datos de especímenes que no sean actualizadas para reflejar el conocimiento cambiante.

Floral heterochrony promotes flexibility of reproductive strategies in the morphologically homogeneous genus Eugenia (Myrtaceae).

Background and Aims: Comparative floral ontogeny represents a valuable tool to understand angiosperm evolution. Such an approach may elucidate subtle changes in development that discretely modify floral architecture and underlie reproductive lability in groups with superficial homogeneous morphology. This study presents a comparative survey of floral development in Eugenia (Myrtaceae), one of the largest genera of angiosperms, and shows how previously undocumented ontogenetic trends help to explain the evolution of its megadiversity in contrast to its apparent flower uniformity. Methods: Using scanning electron microscopy, selected steps of the floral ontogeny of a model species (Eugenia punicifolia) are described and compared with 20 further species representing all ten major clades in the Eugenia phylogenetic tree. Additional floral trait data are contrasted for correlation analysis and character reconstructions performed against the Myrtaceae phylogenetic tree. Key results: Eugenia flowers show similar organ arrangement patterns: radially symmetrical, (most commonly) tetramerous flowers with variable numbers of stamens and ovules. Despite a similar general organization, heterochrony is evident from size differences between tissues and structures at similar developmental stages. These differences underlie variable levels of investment in protection, subtle modifications to symmetry, herkogamic effects and independent androecium and gynoecium variation, producing a wide spectrum of floral display and contributing to fluctuations in fitness. During Eugenia's bud development, the hypanthium (as defined here) is completely covered by stamen primordia, unusual in other Myrtaceae. This is the likely plesiomorphic state for Myrteae and may have represented a key evolutionary novelty in the tribe. Conclusions: Floral evolution in Eugenia depends on heterochronic patterns rather than changes in complexity to promote flexibility in floral strategies. The successful early establishment of Myrteae, previously mainly linked to the key innovation of fleshy fruit, may also have benefitted from changes in flower structure.

Biogeographical patterns of Myrcia s.l. (Myrtaceae) and their correlation with geological and climatic history in the Neotropics.

Many recent studies discuss the influence of climatic and geological events in the evolution of Neotropical biota by correlating these events with dated phylogenetic hypotheses. Myrtaceae is one of the most diverse Neotropical groups and it therefore a good proxy of plant diversity in the region. However, biogeographic studies on Neotropical Myrtaceae are still very limited. Myrcia s.l. is an informal group comprising three accepted genera (Calyptranthes, Marlierea and Myrcia) making up the second largest Neotropical group of Myrtaceae, totalling about 700 species distributed in nine subgroups. Exclusively Neotropical, the group occurs along the whole of the Neotropics with diversity centres in the Caribbean, the Guiana Highlands and the central-eastern Brazil. This study aims to identify the time and place of divergence of Myrcia s.l. lineages, to examine the correlation in light of geological and climatic events in the Neotropics, and to explore relationships among Neotropical biogeographic areas. A dated phylogenetic hypothesis was produced using BEAST and calibrated by placing Paleomyrtinaea princetonensis (56Ma) at the root of the tree; biogeographic analysis used the DEC model with dispersal probabilities between areas based on distance and floristic affinities. Myrcia s.l. originated in the Montane Atlantic Forest between the end of Eocene and early Miocene and this region acted as a secondary cradle for several lineages during the evolution of this group. The Caribbean region was important in the diversification of the Calyptranthes clade while the Guayana shield appears as ancestral area for an older subgroup of Myrcia s.l. The Amazon Forest has relatively low diversity of Myrcia s.l. species but appears to have been important in the initial biogeographic history of old lineages. Lowland Atlantic Forest has high species diversity but species rich lineages did not originate in the area. Diversification of most subgroups of Myrcia s.l. occurred throughout the Miocene, as reported for other Neotropical taxa. During the Miocene, geological events may have influenced the evolution of the Caribbean and Amazon forest lineages, but other regions were geological stable and climate changes were the most likely drivers of diversification. The evolution of many lineages in montane areas suggests that Myrcia s.l. may be particularly adapted to such environments.

Myrteae phylogeny, calibration, biogeography and diversification patterns: Increased understanding in the most species rich tribe of Myrtaceae.

Myrteae (c. 2500 species; 51 genera) is the largest tribe of Myrtaceae and an ecologically important groups of angiosperms in the Neotropics. Systematic relationships in Myrteae are complex, hindering conservation initiatives and jeopardizing evolutionary modelling. A well-supported and robust phylogenetic hypothesis was here targeted towards a comprehensive understanding of the relationships within the tribe. The resultant topology was used as a base for key evolutionary analyses such as age estimation, historical biogeography and diversification rate patterns. One nuclear (ITS) and seven chloroplast (psbA-trnH, matK, ndhF, trnl-trnF, trnQ-rps16, rpl16 and rpl32-trnL) DNA regions for 115 taxa representing 46 out of the 51 genera in the tribe were accessed and analysed using maximum likelihood and Bayesian inference tools for phylogenetic reconstruction. Dates of diversification events were estimated and contrasted using two distinct fossil sets (macro and pollen) in BEAST. The subsequent dated phylogenies were compared and analysed for biogeographical patterns using BioGeoBEARS and diversification rates using BAMM. Myrteae phylogeny presents strong statistical support for three major clades within the tribe: Australasian group, Myrtus group and Main Neotropical Lineage. Dating results from calibration using macrofossil are an average of 20 million years older and show an early Paleocene origin of Myrteae, against a mid-Eocene one from the pollen fossil calibration. Biogeographic analysis shows the origin of Myrteae in Zealandia in both calibration approaches, followed by a widespread distribution throughout the still-linked Gondwana continents and diversification of Neotropical endemic lineages by later vicariance. Best configuration shift indicates three points of acceleration in diversification rates, all of them occurring in the Main Neotropical Lineage. Based on the reconstructed topology, several new taxonomic placements were recovered, including: the relative position of Myrtus communis, the placement of the Blepharocalyx group, the absence of generic endemism in the Caribbean, and the paraphyletism of the former Pimenta group. Distinct calibration approaches affect biogeography interpretation, increasing the number of necessary long distance dispersal events in the topology with older nodes. It is hypothesised that biological intrinsic factors such as modifications of embryo type and polyploidy might have played a role in accelerating shifts of diversification rates in Neotropical lineages. Future perspectives include formal subtribal classification, standardization of fossil calibration approaches and better links between diversification shifts and trait evolution.

The evolutionary history of Eugenia sect. Phyllocalyx (Myrtaceae) corroborates historically stable areas in the southern Atlantic forests.

BACKGROUND AND AIMS: Eugenia sect. Phyllocalyx Nied. includes 14 species endemic to the Neotropics, mostly distributed in the Atlantic coastal forests of Brazil. Here the first comprehensive phylogenetic study of this group is presented, and this phylogeny is used as the basis to evaluate the recent infrageneric classification in Eugenia sensu lato (s.l.) to test the history of the evolution of traits in the group and test hypotheses associated with the history of this clade. METHODS: A total of 42 taxa were sampled, of which 14 were Eugenia sect. Phyllocalyx for one nuclear (ribosomal internal transcribed spacer) and four plastid markers (psbA-trnH, rpl16, trnL-rpl32 and trnQ-rps16). The relationships were reconstructed based on Bayesian analysis and maximum likelihood. Additionally, ancestral area analysis and modelling methods were used to estimate species dispersal, comparing historically climatic stable (refuges) and unstable areas. KEY RESULTS: Maximum likelihood and Bayesian inferences indicate that Eugenia sect. Phyllocalyx is paraphyletic and the two clades recovered are characterized by combinations of morphological characters. Phylogenetic relationships support a link between Cerrado and south-eastern species and a difference in the composition of species from north-eastern and south-eastern Atlantic forest. Refugia and stable areas identified within unstable areas suggest that these areas were important to maintain diversity in the Atlantic forest biodiversity hotspot. CONCLUSION: This study provides a robust phylogenetic framework to address important historical questions for Eugenia s.l. within an evolutionary context, supporting the need for better taxonomic study of one of the largest genera in the Neotropics. Furthermore, valuable insight is offered into diversification and biome shifts of plant species in the highly environmentally impacted Atlantic forest of South America. Evidence is presented that climate stability in the south-eastern Atlantic forest during the Quaternary contributed to the highest levels of plant diversity in this region that acted as a refugium.

Phylogenetic analysis in Myrcia section Aulomyrcia and inferences on plant diversity in the Atlantic rainforest.

BACKGROUND AND AIMS: Myrcia section Aulomyrcia includes ∼120 species that are endemic to the Neotropics and disjunctly distributed in the moist Amazon and Atlantic coastal forests of Brazil. This paper presents the first comprehensive phylogenetic study of this group and this phylogeny is used as a basis to evaluate recent classification systems and to test alternative hypotheses associated with the history of this clade. METHODS: Fifty-three taxa were sampled out of the 120 species currently recognized, plus 40 outgroup taxa, for one nuclear marker (ribosomal internal transcribed spacer) and four plastid markers (psbA-trnH, trnL-trnF, trnQ-rpS16 and ndhF). The relationships were reconstructed based on Bayesian and maximum likelihood analyses. Additionally, a likelihood approach, 'geographic state speciation and extinction', was used to estimate region- dependent rates of speciation, extinction and dispersal, comparing historically climatic stable areas (refugia) and unstable areas. KEY RESULTS: Maximum likelihood and Bayesian inferences indicate that Myrcia and Marlierea are polyphyletic, and the internal groupings recovered are characterized by combinations of morphological characters. Phylogenetic relationships support a link between Amazonian and north-eastern species and between north-eastern and south-eastern species. Lower extinction rates within glacial refugia suggest that these areas were important in maintaining diversity in the Atlantic forest biodiversity hotspot. CONCLUSIONS: This study provides a robust phylogenetic framework to address important ecological questions for Myrcia s.l. within an evolutionary context, and supports the need to unite taxonomically the two traditional genera Myrcia and Marlierea in an expanded Myrcia s.l. Furthermore, this study offers valuable insights into the diversification of plant species in the highly impacted Atlantic forest of South America; evidence is presented that the lowest extinction rates are found inside refugia and that range expansion from unstable areas contributes to the highest levels of plant diversity in the Bahian refugium.

A new R package to parse plant species occurrence records into unique collection events efficiently reduces data redundancy.

Biodiversity data aggregators, such as Global Biodiversity Information Facility (GBIF) suffer from inflation of the number of occurrence records when data from different databases are merged but not fully reconciled. The ParseGBIF workflow is designed to parse duplicate GBIF species occurrence records into unique collection events (gatherings) and to optimise the quality of the spatial data associated with them. ParseGBIF provides tools to verify and standardize species scientific names according to the World Checklist of Vascular Plants taxonomic backbone, and to parse duplicate records into unique 'collection events', in the process compiling the most informative spatial data, where more than one duplicate is available, and providing crude estimates of taxonomic and spatial data quality. When GBIF occurrence records for a medium-sized vascular plant family, the Myrtaceae, were processed by ParseGBIF, the average number of records useful for spatial analysis increased by 180%. ParseGBIF could therefore be valuable in the evaluation of species' occurrences at the national scale in support for national biodiversity plans, identification of plant areas important for biodiversity, sample bias estimation to inform future sampling efforts, and to forecast species range shifts in response to global climate change.

Machine learning enhances prediction of plants as potential sources of antimalarials.

Plants are a rich source of bioactive compounds and a number of plant-derived antiplasmodial compounds have been developed into pharmaceutical drugs for the prevention and treatment of malaria, a major public health challenge. However, identifying plants with antiplasmodial potential can be time-consuming and costly. One approach for selecting plants to investigate is based on ethnobotanical knowledge which, though having provided some major successes, is restricted to a relatively small group of plant species. Machine learning, incorporating ethnobotanical and plant trait data, provides a promising approach to improve the identification of antiplasmodial plants and accelerate the search for new plant-derived antiplasmodial compounds. In this paper we present a novel dataset on antiplasmodial activity for three flowering plant families - Apocynaceae, Loganiaceae and Rubiaceae (together comprising c. 21,100 species) - and demonstrate the ability of machine learning algorithms to predict the antiplasmodial potential of plant species. We evaluate the predictive capability of a variety of algorithms - Support Vector Machines, Logistic Regression, Gradient Boosted Trees and Bayesian Neural Networks - and compare these to two ethnobotanical selection approaches - based on usage as an antimalarial and general usage as a medicine. We evaluate the approaches using the given data and when the given samples are reweighted to correct for sampling biases. In both evaluation settings each of the machine learning models have a higher precision than the ethnobotanical approaches. In the bias-corrected scenario, the Support Vector classifier performs best - attaining a mean precision of 0.67 compared to the best performing ethnobotanical approach with a mean precision of 0.46. We also use the bias correction method and the Support Vector classifier to estimate the potential of plants to provide novel antiplasmodial compounds. We estimate that 7677 species in Apocynaceae, Loganiaceae and Rubiaceae warrant further investigation and that at least 1300 active antiplasmodial species are highly unlikely to be investigated by conventional approaches. While traditional and Indigenous knowledge remains vital to our understanding of people-plant relationships and an invaluable source of information, these results indicate a vast and relatively untapped source in the search for new plant-derived antiplasmodial compounds.

A Taxonomically-verified and Vouchered Checklist of the Vascular Plants of the Republic of Guinea.

The Checklist of the Vascular Plants of the Republic of Guinea (CVPRG) is a specimen-based, expert-validated knowledge product, which provides a concise synthesis and overview of current knowledge on 3901 vascular plant species documented from Guinea (Conakry), West Africa, including their accepted names and synonyms, as well as their distribution and status within Guinea (indigenous or introduced, endemic or not). The CVPRG is generated automatically from the Guinea Collections Database and the Guinea Names Backbone Database, both developed and maintained at the Royal Botanic Gardens, Kew, in collaboration with the staff of the National Herbarium of Guinea. A total of 3505 indigenous vascular plant species are reported of which 3328 are flowering plants (angiosperms); this represents a 26% increase in known indigenous angiosperms since the last floristic overview. Intended as a reference for scientists documenting the diversity and distribution of the Guinea flora, the CVPRG will also inform those seeking to safeguard the rich plant diversity of Guinea and the societal, ecological and economic benefits accruing from these biological resources.

Phylogenetic Relationships Within the Hyper-Diverse Genus Eugenia (Myrtaceae: Myrteae) Based on Target Enrichment Sequencing.

Eugenia is one of the most taxonomically challenging lineages of flowering plants, in which morphological delimitation has changed over the last few years resulting from recent phylogenetic study based on molecular data. Efforts, until now, have been limited to Sanger sequencing of mostly plastid markers. These phylogenetic studies indicate 11 clades formalized as infrageneric groups. However, relationships among these clades are poorly supported at key nodes and inconsistent between studies, particularly along the backbone and within Eugenia sect. Umbellatae encompasses ca. 700 species. To resolve and better understand systematic discordance, 54 Eugenia taxa were subjected to phylogenomic Hyb-Seq using 353 low-copy nuclear genes. Twenty species trees based on coding and non-coding loci of nuclear and plastid datasets were recovered using coalescent and concatenated approaches. Concordant and conflicting topologies were assessed by comparing tree landscapes, topology tests, and gene and site concordance factors. The topologies are similar except between nuclear and plastid datasets. The coalescent trees better accommodate disparity in the intron dataset, which contains more parsimony informative sites, while concatenated trees recover more conservative topologies, as they have narrower distribution in the tree landscape. This suggests that highly supported phylogenetic relationships determined in previous studies do not necessarily indicate overwhelming concordant signal. Congruence must be interpreted carefully especially in concatenated datasets. Despite this, the congruence between the multi-species coalescent (MSC) approach and concatenated tree topologies found here is notable. Our analysis does not support Eugenia subg. Pseudeugenia or sect. Pilothecium, as currently circumscribed, suggesting necessary taxonomic reassessment. Five clades are further discussed within Eugenia sect. Umbellatae progress toward its division into workable clades. While targeted sequencing provides a massive quantity of data that improves phylogenetic resolution in Eugenia, uncertainty still remains in Eugenia sect. Umbellatae. The general pattern of higher site coefficient factor (CF) than gene CF in the backbone of Eugenia suggests stochastic error from limited signal. Tree landscapes in combination with concordance factor scores, as implemented here, provide a comprehensive approach that incorporates several phylogenetic hypotheses. We believe the protocols employed here will be of use for future investigations on the evolutionary history of Myrtaceae.

Botanical Monography in the Anthropocene.

Unprecedented changes in the Earth's biota are prompting urgent efforts to describe and conserve plant diversity. For centuries, botanical monographs - comprehensive systematic treatments of a family or genus - have been the gold standard for disseminating scientific information to accelerate research. The lack of a monograph compounds the risk that undiscovered species become extinct before they can be studied and conserved. Progress towards estimating the Tree of Life and digital information resources now bring even the most ambitious monographs within reach. Here, we recommend best practices to complete monographs urgently, especially for tropical plant groups under imminent threat or with expected socioeconomic benefits. We also highlight the renewed relevance and potential impact of monographies for the understanding, sustainable use, and conservation of biodiversity.