To move or to evolve: contrasting patterns of intercontinental connectivity and climatic niche evolution in "Terebinthaceae" (Anacardiaceae and Burseraceae)

Three complete chloroplast genomes from two north American Rhus species and phylogenomics of Anacardiaceae

BACKGROUND

The suamc genus Rhus (sensu stricto) includes two subgenera, Lobadium (ca. 25 spp.) and Rhus (ca. 10 spp.). Their members, R. glabra and R. typhina (Rosanae: Sapindales: Anacardiaceae), are two economic important species. Chloroplast genome information is of great significance for the study of plant phylogeny and taxonomy.

RESULTS

The three complete chloroplast genomes from two Rhus glabra and one R. typhina accessions were obtained with a total of each about 159k bp in length including a large single-copy region (LSC, about 88k bp), a small single-copy regions (SSC, about 19k bp) and a pair of inverted repeats regions (IRa/IRb, about 26k bp), to form a canonical quadripartite structure. Each genome contained 88 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes. The overall GC content of the three genomes all were same (37.8%), and RSCU values showed that they all had the same codon prefers, i.e., to use codon ended with A/U (93%) except termination codon. Three variable hotspots, i.e., ycf4-cemA, ndhF-rpl32-trnL and ccsA-ndhD, and a total of 152-156 simple sequence repeats (SSR) were identified. The nonsynonymous (Ka)/synonymous (Ks) ratio was calculated, and cemA and ycf2 genes are important indicators of gene evolution. The phylogenetic analyses of the family Anacardiaceae showed that the eight genera were grouped into three clusters, and supported the monophyly of the subfamilies and all the genera. The accessions of five Rhus species formed four clusters, while, one individual of R. typhina grouped with the R. glabra accessions instead of clustering into the two other individuals of R. typhina in the subgenus Rhus, which showed a paraphyletic relationship.

CONCLUSIONS

Comparing the complete chloroplast genomes of the Rhus species, it was found that most SSRs were A/T rich and located in the intergenic spacer, and the nucleotide divergence exhibited higher levels in the non-coding region than in the coding region. The Ka/Ks ratio of cemA gene was > 1 for species collected in America, while it was < 1 for other species in China, which dedicated that the Rhus species from North America and East Asia have different evolutionary pressure. The phylogenetic analysis of the complete chloroplast genome clarified the Rhus placement and relationship. The results obtained in this study are expected to provide valuable genetic resources to perform species identification, molecular breeding, and intraspecific diversity of the Rhus species.

Climatic and biogeographic processes underlying the diversification of the pantropical flowering plant family Annonaceae

Tropical forests harbor the richest biodiversity among terrestrial ecosystems, but few studies have addressed the underlying processes of species diversification in these ecosystems. We use the pantropical flowering plant family Annonaceae as a study system to investigate how climate and biogeographic events contribute to diversification. A super-matrix phylogeny comprising 835 taxa (34% of Annonaceae species) based on eight chloroplast regions was used in this study. We show that global temperature may better explain the recent rapid diversification in Annonaceae than time and constant models. Accelerated accumulation of niche divergence (around 15 Ma) lags behind the increase of diversification rate (around 25 Ma), reflecting a heterogeneous transition to recent diversity increases. Biogeographic events are related to only two of the five diversification rate shifts detected. Shifts in niche evolution nevertheless appear to be associated with increasingly seasonal environments. Our results do not support the direct correlation of any particular climatic niche shifts or historical biogeographical event with shifts in diversification rate. Instead, we suggest that Annonaceae diversification can lead to later niche divergence as a result of increasing interspecific competition arising from species accumulation. Shifts in niche evolution appear to be associated with increasingly seasonal environments. Our results highlight the complexity of diversification in taxa with long evolutionary histories.

First fossil woods and palm stems from the mid-Paleocene of Myanmar and implications for biogeography and wood anatomy

PREMISE

The rise of angiosperm-dominated tropical rainforests has been proposed to have occurred shortly after the Cretaceous-Paleogene transition. Paleocene fossil wood assemblages are rare yet provide important data for understanding these forests and whether their wood anatomical features can be used to document the changes that occurred during this transition.

METHODS

We used standard techniques to section 11 fossil wood specimens of Paleocene-age, described the anatomy using standard terminology, and investigated their affinities to present-day taxa.

RESULTS

We report here the first middle Paleocene fossil wood specimens from Myanmar, which at the time was near the equator and anchored to India. Some fossils share affinities with Arecaceae, Sapindales (Anacardiaceae, Meliaceae) and Moraceae and possibly Fabaceae or Lauraceae. One specimen is described as a new species and genus: Compitoxylon paleocenicum gen. et sp. nov.

CONCLUSIONS

This assemblage reveals the long-lasting presence of these aforementioned groups in South Asia and suggests the early presence of multiple taxa of Laurasian affinity in Myanmar and India. The wood anatomical features of the dicotyledonous specimens reveal that both "modern" and "primitive" features (in a Baileyan scheme) are present with proportions similar to features in specimens from Paleocene Indian localities. Their anatomical diversity corroborates that tropical flora display "modern" features early in the history of angiosperms and that their high diversity remained steady afterward.

Chemical and cytotoxicity profiles of 11 pink pepper (Schinus spp.) samples via non-targeted hyphenated high-performance thin-layer chromatography

INTRODUCTION

Pink pepper is a worldwide used spice that corresponds to the berries of two species, Schinus terebinthifolia Raddi or S. molle L. (Anacardiaceae). Toxic and allergic reactions by ingestion or contact with these plants were reported, and classical in vitro studies have highlighted the cytotoxic properties of apolar extracts from the fruits.

OBJECTIVES

Perform a non-targeted screening of 11 pink pepper samples for the detection and identification of individual cytotoxic substances.

METHODS

After reversed-phase high-performance thin-layer chromatography (RP-HPTLC) separation of the extracts and multi-imaging (UV/Vis/FLD), cytotoxic compounds were detected by bioluminescence reduction from luciferase reporter cells (HEK 293 T-CMV-ELuc) applied directly on the adsorbent surface, followed by elution of detected cytotoxic substance into atmospheric-pressure chemical ionization high-resolution mass spectrometry (APCI-HRMS).

RESULTS

Separations for mid-polar and non-polar fruit extracts demonstrated the selectivity of the method to different substance classes. One cytotoxic substance zone was tentatively assigned as moronic acid, a pentacyclic triterpenoid acid.

CONCLUSION

The developed non-targeted hyphenated RP-HPTLC-UV/Vis/FLD-bioluminescent cytotoxicity bioassay-FIA-APCI-HRMS method was successfully demonstrated for cytotoxicity screening (bioprofiling) and respective cytotoxin assignment.

Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication

Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order's spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.

Edaphic specialization onto bare, rocky outcrops as a factor in the evolution of desert angiosperms

Understanding the processes that enable organisms to shift into more arid environments as they emerge is critical for gauging resilience to climate change, yet these forces remain poorly known. In a comprehensive clade-based study, we investigate recent shifts into North American deserts in the rock daisies (tribe Perityleae), a diverse tribe of desert sunflowers (Compositae). We sample rock daisies across two separate contact zones between tropical deciduous forest and desert biomes in western North America and infer a time-calibrated phylogeny based on target capture sequence data. We infer biome shifts using Bayesian inference with paleobiome-informed models and find evidence for seven independent shifts into desert habitats since the onset of aridification in the late Miocene. The earliest shift occurred out of tropical deciduous forests and led to an extensive radiation throughout North American deserts that accounts for the majority of extant desert rock daisies. Estimates of life history and micro-habitat in the rock daisies reveal a correlation between a suffrutescent perennial life history and edaphic endemism onto rocky outcrops, an ecological specialization that evolved prior to establishment and diversification in deserts. That the insular radiation of desert rock daisies stemmed from ancestors preadapted for dry conditions as edaphic endemics in otherwise densely vegetated tropical deciduous forests in northwest Mexico underscores the crucial role of exaptation and dispersal for shifts into arid environments.

The complete plastome of Spondias dulcis (Anacardiaceae): an edible deciduous tree species from South America

Spondias dulcis is a deciduous tree in the family Anacardiaceae. The species originates in South America and now is widely cultivated in tropical areas due to its edible fruits. In this study, we find that the length of the complete plastome of S. dulcis is 162,256 bp. It includes 35 tRNA genes and eight rRNA genes, 86 protein-coding genes and totally 130 genes. The complete plastome of S. dulcis includes a small single-copy (SSC) region of 18,459 bp, a large single-copy (LSC) region of 89,353 bp, and two inverted repeats (IRs) regions of 27,222 bp. The total G/C content of S. dulcis is 37.7%. It shows that S. dulcis is closely related to S. mombin within Anacardiaceae. It will contribute to the conservation genetics of S. dulcis and the phylogenetic studies in Anacardiaceae.

Fruit Anatomy of the Canarieae (Burseraceae)

Fruits historically have been the key character for delimitation of tribes in the Burseraceae. However, fruit structure is incompletely known within the family, thus the importance of this character is unclear. This study of fruit anatomy in the traditional tribe Canarieae examines the distribution of the tissues that correspond to the exo-, meso-, and endocarp. The detailed arrangement and measurement of the tissues are reported here for the first time in all eight genera in the tribe. The evidence suggests that in all cases except Pseudodacryodes, the endocarp has at least one layer of parenchyma cells within which a sclereid layer is evident and, in some cases, an inner epidermis. All Canarieae fruits exhibit secretory canals, and some taxa have epidermal glands with resin-like contents. Evidence of carpellar sutures was found for all Canarieae, and in Dacryodes, Haplolobus, Rosselia, and Santiria, an articulated plate is present that corresponds to an abortive locule. The anatomical and morphological characters presented here are useful in delimiting genera within Canarieae.

A new Oligocene-Miocene tree from Panama and historical Anacardium migration patterns

Migration of Boreotropical megathermal taxa during the Oligocene and Miocene played a key role in assembling diversity in tropical regions. Despite scattered fossil reports, the cashew genus Anacardium offers an excellent example of such migration. The fossil woods described here come from localities in Veraguas, Panama mapped as Oligocene-Miocene. We studied, described, and identified two well-preserved specimens using wood anatomical characteristics and completed extensive comparisons between fossil and extant material. The studied fossil woods share several diagnostic features with the modern Anacardium genus, including large solitary vessels, large intervessel-pitting, a simple vessel-ray pitting pattern, and mostly 1–3 seriate rays with large rhomboidal solitary crystals. We propose a new fossil species named Anacardium gassonii sp. nov., that adds an essential piece to the understanding of the historical biogeography of the genus. In addition, our findings confirm previous interpretations of this species’ migration from Europe to North America and its crossing through Panama, leading to subsequent diversification in South America. This discovery provides an important link to the historical migration patterns of the genus, supporting the notion of an Eocene migration to the Neotropics via Boreotropical bridges, as well as an Oligocene-Miocene crossing of Central America followed by diversification in South America.

Complete chloroplast genome of Myracrodruon urundeuva and its phylogenetics relationships in Anacardiaceae family

Continuous exploratory use of tree species is threatening the existence of several plants in South America. One of these threatened species is Myracroduron urundeuva, highly exploited due to the high quality and durability of its wood. The chloroplast (cp) has been used for several evolutionary studies as well traceability of timber origin, based on its gene sequences and simple sequence repeats (SSR) variability. Cp genome organization is usually consisting of a large single copy and a small single copy region separated by two inverted repeats regions. We sequenced the complete cp genome from M. urundeuva based on Illumina next-generation sequencing. Our results show that the cp genome is 159,883 bp in size. The 36 SSR identified ranging from mono- to hexanucleotides. Positive selection analysis revealed nine genes related to photosystem, protein synthesis, and DNA replication, and protease are under positive selection. Genome comparison a other Anacardiaceae chloroplast genomes showed great variability in the family. The phylogenetic analysis using complete chloroplast genome sequences of other Anacardiaceae family members showed a close relationship with two other economically important genera, Pistacia and Rhus. These results will help future investigations of timber monitoring and population and evolutionary studies.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00989-1.

The effect of single biome occupancy on the estimation of biome shifts and the detection of biome conservatism

Biome conservatism is often regarded as common in diversifying lineages, based on the detection of low biome shift rates or high phylogenetic signal. However, many studies testing biome conservatism utilise a single-biome-per-species approach, which may influence the detection of biome conservatism. Meta-analyses show that biome shift rates are significantly lower (less than a tenth), when single biome occupancy approaches are adopted. Using New Zealand plant lineages, estimated biome shifts were also significantly lower (14-67% fewer biome shifts) when analysed under the assumption of a single biome per species. Although a single biome approach consistently resulted in lower biome shifts, it detected fewer instances of biome conservatism. A third of clades (3 out of 9) changed status in biome conservatism tests between single and multiple biome occupancy approaches, with more instances of significant biome conservatism when using a multiple biome occupancy approach. A single biome approach may change the likelihood of finding biome conservatism because it assumes biome specialisation within species, falsely recognises some biome shift types and fails to include other biome shift types. Our results indicate that the degree of biome fidelity assumed has a strong influence on analyses assessing biome shift rates, and biome conservatism testing. We advocate analyses that allow species to occupy multiple biomes.

Habitat Specificity, Host Plants and Areas of Endemism for the Genera-Group Blepharida s.l. in the Afrotropical Region (Coleoptera, Chrysomelidae, Galerucinae, Alticini)

Simple Summary

Knowledge of the processes that generate biodiversity is a core-issue of any conservation strategy because it allows predicting the effects of environmental changes in the number and distribution of target taxa. Some phytophagous insects can be good potential indicators of such processes, thanks to their wide distribution and their sensitivity to climate change, due to the association with specific environments and host plants. Unfortunately, this ecological information is often lacking. However, statistical tools allow reconstructing the ecological features of interest, based on the presence–absence data of the taxa, the climatic and vegetational features of their distributional areas, and the available data about their host plants. In this paper, we apply some geostatistical methods to identify processes and patterns of biodiversity at a continental scale, focusing on a group of phytophagous insects widespread in sub-Saharan Africa.

Abstract

The genus Calotheca Heyden (Chrysomelidae) is mainly distributed in the eastern and southern parts of sub-Saharan Africa, with some extensions northward, while Blepharidina Bechyné occurs in the intertropical zone of Africa, with two subgenera, Blepharidina s. str. and Blepharidina(Afroblepharida) Biondi and D’Alessandro. These genera show different ecological preferences. Through an up-to-date presence–absence dataset, in the light of the terrestrial ecoregions of sub-Saharan Africa and the distribution of their possible host plants, we interpreted the pattern of occurrence of these three supraspecific taxa, by geostatistical analyses in GIS and R environments. The separation of Blepharidina from Calotheca was probably driven by changes in climate as adaptation to more xeric and warm environments with a major occupancy of semidesert and savannah habitats, especially in the Afroblepharida species. Based on our data and analyses, Calotheca is mainly associated with Searsia (Anacardiaceae), and Blepharidina is likely associated with Commiphora (Burseraceae). This hypothesis is also corroborated by the widespread and even dominance of the Commiphora plants in the ecoregions where both Blepharidina s.str. and, above all, Afroblepharida, are more common. The main areas of endemism of the two genera are also differently located: Calotheca in the temperate zone; Blepharidina within the intertropical belt.

Phylotranscriptomics reveals the complex evolutionary and biogeographic history of the genus Tsuga with an East Asian-North American disjunct distribution

The disjunct distribution between East Asia and North America is one of the best established biogeographic patterns. A robust phylogeny is fundamental for understanding the biogeographic histories of taxa with this distribution pattern. Tsuga (hemlock) is a genus of Pinaceae with a typical intercontinental disjunct distribution in East Asia and eastern and western North America, and its phylogeny has not been completely reconstructed in previous studies. In this study, we reconstructed a highly resolved phylogeny of Tsuga using 881 nuclear genes, 60 chloroplast genes and 23 mitochondrial genes and explored its biogeographic and reticulate evolutionary history. The results of phylogenetic analysis, molecular dating and ancestral area reconstruction indicate that Tsuga very likely originated from North America in the late Oligocene and dispersed from America to East Asia via the Bering Land Bridge during the middle Miocene. In particular, we found complex reticulate evolutionary pattern among the East Asian hemlock species. T. sieboldii possibly originated from hybridization with the ancestor of T. chinensis from mainland China and T. forrestii as the paternal donor and the ancestor of T. diversifolia and T. ulleungensis as the maternal donor. T. chinensis (Taiwan) could have originated by hybridization together with T. sieboldii and then evolved independently after dispersal to the Taiwan Island, subsequently experiencing mitochondrial DNA introgression with T. chinensis from mainland China. Moreover, our study found that T. chinensis from western China is more closely related to T. forrestii than to T. chinensis from eastern China. The nonmonophyletic T. chinensis needs taxonomic reconsideration.

Modeling Phylogenetic Biome Shifts on a Planet with a Past

The spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time, we developed a phylogenetic biome shift model in which each lineage shifts between biomes and disperses between regions at rates that depend on the lineage's biome affinity and location relative to the spatial distribution of biomes at any given time. To study the behavior of the biome shift model in an empirical setting, we developed a literature-based representation of paleobiome structure for three mesic forest biomes, six regions, and eight time strata, ranging from the Late Cretaceous (100 Ma) through the present. We then fitted the model to a time-calibrated phylogeny of 119 Viburnum species to compare how the results responded to various realistic or unrealistic assumptions about paleobiome structure. Ancestral biome estimates that account for paleobiome dynamics reconstructed a warm temperate (or tropical) origin of Viburnum, which is consistent with previous fossil-based estimates of ancestral biomes. Imposing unrealistic paleobiome distributions led to ancestral biome estimates that eliminated support for tropical origins, and instead inflated support for cold temperate ancestry throughout the warmer Paleocene and Eocene. The biome shift model we describe is applicable to the study of evolutionary systems beyond Viburnum, and the core mechanisms of our model are extensible to the design of richer phylogenetic models of historical biogeography and/or lineage diversification. We conclude that biome shift models that account for dynamic geographical opportunities are important for inferring ancestral biomes that are compatible with our understanding of Earth history.[Ancestral states; biome shifts; historical biogeography; niche conservatism; phylogenetics].

Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L

Plastid genomes (plastomes) represent rich sources of information for phylogenomics, from higher-level studies to below the species level. The genus Rhus (sumac) has received a significant amount of study from phylogenetic and biogeographic perspectives, but genomic studies in this genus are lacking. Rhus integrifolia and R. ovata are two shrubby species of high ecological importance in the southwestern USA and Mexico, where they occupy coastal scrub and chaparral habitats. They hybridize frequently, representing a fascinating system in which to investigate the opposing effects of hybridization and divergent selection, yet are poorly characterized from a genomic perspective. In this study, complete plastid genomes were sequenced for one accession of R. integrifolia and one each of R. ovata from California and Arizona. Sequence variation among these three accessions was characterized, and PCR primers potentially useful in phylogeographic studies were designed. Phylogenomic analyses were conducted based on a robustly supported phylogenetic framework based on 52 complete plastomes across the order Sapindales. Repeat content, rather than the size of the inverted repeat, had a stronger relative association with total plastome length across Sapindales when analyzed with phylogenetic least squares regression. Variation at the inverted repeat boundary within Rhus was striking, resulting in major shifts and independent gene losses. Specifically, rps19 was lost independently in the R. integrifolia-ovata complex and in R. chinensis, with a further loss of rps22 and a major contraction of the inverted repeat in two accessions of the latter. Rhus represents a promising novel system to study plastome structural variation of photosynthetic angiosperms at and below the species level.

Joint Phylogenetic Estimation of Geographic Movements and Biome Shifts during the Global Diversification of Viburnum

Phylogeny, molecular sequences, fossils, biogeography, and biome occupancy are all lines of evidence that reflect the singular evolutionary history of a clade, but they are most often studied separately, by first inferring a fossil-dated molecular phylogeny, then mapping on ancestral ranges and biomes inferred from extant species. Here we jointly model the evolution of biogeographic ranges, biome affinities, and molecular sequences, while incorporating fossils to estimate a dated phylogeny for all of the 163 extant species of the woody plant clade Viburnum (Adoxaceae) that we currently recognize in our ongoing worldwide monographic treatment of the group. Our analyses indicate that while the major Viburnum lineages evolved in the Eocene, the majority of extant species originated since the Miocene. Viburnum radiated first in Asia, in warm, broad-leaved evergreen (lucidophyllous) forests. Within Asia, we infer several early shifts into more tropical forests, and multiple shifts into forests that experience prolonged freezing. From Asia, we infer two early movements into the New World. These two lineages probably first occupied warm temperate forests and adapted later to spreading cold climates. One of these lineages (Porphyrotinus) occupied cloud forests and moved south through the mountains of the Neotropics. Several other movements into North America took place more recently, facilitated by prior adaptations to freezing in the Old World. We also infer four disjunctions between Asia and Europe: the Tinus lineage is the oldest and probably occupied warm forests when it spread, whereas the other three were more recent and in cold-adapted lineages. These results variously contradict published accounts, especially the view that Viburnum radiated initially in cold forests and, accordingly, maintained vessel elements with scalariform perforations. We explored how the location and biome assignments of fossils affected our inference of ancestral areas and biome states. Our results are sensitive to, but not entirely dependent upon, the inclusion of fossil biome data. It will be critical to take advantage of all available lines of evidence to decipher events in the distant past. The joint estimation approach developed here provides cautious hope even when fossil evidence is limited. [Biogeography; biome; combined evidence; fossil pollen; phylogeny; Viburnum.].

Assembly rules in a resource gradient: Competition and abiotic filtering determine the structuring of plant communities in stressful environments

The relative importance of different community assembly mechanisms varies depending on the environment. According to the stress-dominance hypothesis (SDH), assembly mechanisms range from strong abiotic filtering to competition as the environment becomes more favourable. Most evidence for the SDH comes from studies in gradients of conditions (i.e. abiotic environmental factors that influence the functioning of organisms but are not consumed by them). However, we hypothesized that in resource gradients, competition increases as abiotic filtering becomes stronger. To test our hypothesis, we set up eight plots at different sites along an abiotic severity gradient in the Brazilian semi-arid region (BSAR). In each plot, we identified and measured each woody plant species found, and we recorded 11 functional traits of the main species, dividing the traits into alpha (competition effects) and beta (abiotic filtering effects). We investigated the presence of phylogenetic signal in the traits, the community phylogenetic and phenotypic patterns, and associated the variation in these patterns with the availability of water and soil nutrients. We found phylogenetic signal for most (91%) of the traits analysed. The phylogenetic patterns varied from clustered in stressful sites to random or overdispersed in favourable sites, and we concluded that these phylogenetic patterns were the result of historical processes influencing community assembly in different environments in the BSAR. In general, the phenotypic patterns varied from clustered at the most stressful end to random at less stressful sites. Our results show that in resource gradients, any restriction of the resource (hydric or edaphic) intensifies abiotic filtering and, at the same time, increases the competitive hierarchy among species. On the other hand, stochastic processes seem to have a stronger influence under more favourable abiotic conditions, where abiotic filtering and competition are weaker. Thus, we conclude that the SDH is not supported in resource gradients.

The Dispersion of Diaspores of Protium icicariba (Burseraceae) - a Networked or Multifactorial System?

The adaptive radiation of the angiosperms was strongly affected by fruit and seed dispersal since the establishment of the seedlings is a fundamental process for the recruitment of juveniles to the populations. Among the species of Burseraceae, seeds with fleshy attachments and high caloric value suggest mammaliochory as an ancestral dispersal way. In Protium icicariba, at the same time as there is a visual pattern typical of ornithochory, with a report of effective demonstration, the diaspores present the highest levels of essential oils of the whole plant, suggesting other dispersion processes by olfactory guided vectors. This work aims to monitor the diasporic dispersal process in P. icicariba in situ, aiming to identify dispersers and to investigate the role of the essential oil in the dispersion of diaspores of this plant species. The natural dispersion was monitored in situ, in weekly campaigns throughout eight months, using visual and photographic records, in daily shifts of six hours, distributed along the dawn, morning, afternoon, dusk, and night. We used both direct observation and continuous picture capturing along 43 days with photographic traps. Mature diaspores removed from pseudocapsules were pooled to determine potential dispersers. Artificial models of the diaspores, in white and green colors, were also used to test hypotheses on the role of scent in the dispersion, added 1%, weight/weight, of the essential oil extracted from the mature diaspores, which chemical composition determined by gas chromatography coupled to mass spectrometry. Besides, the analysis of stomach contents of lizards collected in adjacent area was also performed. In daytime and nighttime monitoring in nature, no vertebrates were recorded dispersing diaspores. The most common was the primary wind-facilitated autochory of diaspores to the substrate, near the plant matrices. Secondarily, workers of the ant species Atta robusta can remove the pseudoarils or move the pyrenes to the anthills. The lizard species Tropidurus torquatus ingests pyrenes with the pseudoarils, and the sclerified pericarp of the pyrene is potentially resistant to chemical action of the digestive juices. Ants and lizards have also accessed the caves with natural diaspores. Concerning the artificial diaspore models, ants accessed, indistinctly, white and the green models that contained essential oils. The lizards accessed the white models, with or without essential oils, and showed insignificant access to green ones, with or without essential oil. The ingestion of pyrenes by lizards was also confirmed through analysis of stomach contents. The aggregate spatial pattern of P. icicariba at the study site, associated with clumps, may be derived from germination in the substrate near the matrices, or in the anthills or after diaspora defecation and / or regurgitation of the lizard, which is a species strongly associated with clumps of this vegetation. As the access to the diaspores by ants and lizards depends on the primary autochory, and no impediments to the germination near to the matrix plant were found, the dispersion is compatible with a multifactorial characteristic of the diplochory.

Global Succulent Biome phylogenetic conservatism across the pantropical Caesalpinia Group (Leguminosae)

The extent to which phylogenetic biome conservatism vs biome shifting determines global patterns of biodiversity remains poorly understood. To address this question, we investigated the biogeography and trajectories of biome and growth form evolution across the Caesalpinia Group (Leguminosae), a clade of 225 species of trees, shrubs and lianas distributed across the Rainforest, Succulent, Temperate and Savanna Biomes. We focused especially on the little-known Succulent Biome, an assemblage of succulent-rich, grass-poor, seasonally dry tropical vegetation distributed disjunctly across the Neotropics, Africa, Arabia and Madagascar. We reconstructed a time-calibrated phylogeny, assembled species occurrence data and assigned species to areas, biomes and growth forms. These data are used to estimate the frequency of transcontinental disjunctions, biome shifts and evolutionary transitions between growth forms and test for phylogenetic biome conservatism and correlated evolution of growth forms and biome shifts. We uncovered a pattern of strong phylogenetic Succulent Biome conservatism. We showed that transcontinental disjunctions confined within the Succulent Biome are frequent and that biome shifts to the Savanna, Rainforest and Temperate Biomes are infrequent and closely associated with shifts in plant growth forms. Our results suggest that the Succulent Biome comprises an ecologically constrained evolutionary arena spanning large geographical disjunctions across the tropics.

Changing Ecological Opportunities Facilitated the Explosive Diversification of New Caledonian Oxera (Lamiaceae)

Phylogenies recurrently demonstrate that oceanic island systems have been home to rapid clade diversification and adaptive radiations. The existence of adaptive radiations posits a central role of natural selection causing ecological divergence and speciation, and some plant radiations have been highlighted as paradigmatic examples of such radiations. However, neutral processes may also drive speciation during clade radiations, with ecological divergence occurring following speciation. Here, we document an exceptionally rapid and unique radiation of Lamiaceae within the New Caledonian biodiversity hotspot. Specifically, we investigated various biological, ecological, and geographical drivers of species diversification within the genus Oxera. We found that Oxera underwent an initial process of rapid cladogenesis likely triggered by a dramatic period of aridity during the early Pliocene. This early diversification of Oxera was associated with an important phase of ecological diversification triggered by significant shifts of pollination syndromes, dispersal modes, and life forms. Finally, recent diversification of Oxera appears to have been further driven by the interplay of allopatry and habitat shifts likely related to climatic oscillations. This suggests that Oxera could be regarded as an adaptive radiation at an early evolutionary stage that has been obscured by more recent joint habitat diversification and neutral geographical processes. Diversification within Oxera has perhaps been triggered by varied ecological and biological drivers acting in a leapfrog pattern, but geographic processes may have been an equally important driver. We suspect that strictly adaptive radiations may be rare in plants and that most events of rapid clade diversification may have involved a mixture of geographical and ecological divergence.

Osmophores and floral fragrance in Anacardium humile and Mangifera indica (Anacardiaceae): an overlooked secretory structure in Sapindales

Flowers of Anacardiaceae and other Sapindales typically produce nectar, but scent, often associated with a reward for pollinators, has surprisingly been mentioned only rarely for members of the family and order. However, flowers of Anacardium humile and Mangifera indica produce a strong sweet scent. The origin and composition of these floral scents is the subject of this study. Screening of potential osmophores on the petals and investigations of their anatomy were carried out by light, scanning and transmission electron microscopy. The composition of the floral fragrance was characterized by gas chromatography-mass spectrometry. In both species, the base of the adaxial side of each petal revealed specialized secretory epidermal cells which are essentially similar in structure and distinct from all other neighbouring cells. These cells also showed evidence of granulocrine secretory mechanisms and slight specific variations in their subcellular apparatus coinciding with the respective composition of the floral fragrance, predominantly composed of sesquiterpenes in A. humile and monoterpenes in M. indica. This study reports the presence of osmophores for the first time in flowers of Anacardiaceae and confirms the link between the ultrastructural features of their secretory cells and the volatiles produced by the flowers. The flowers of most Sapindales, including Anacardiaceae, are nectariferous. However, the presence of osmophores has only been described for very few genera of Rutaceae and Sapindaceae. Both the occurrence of osmophores and fragrance may have largely been overlooked in Anacardiaceae and Sapindales until now. Further studies are needed to better understand the nature and diversity of the interactions of their nectariferous flowers with their pollinators.

Phylogeny of Schinus L. (Anacardiaceae) with a new infrageneric classification and insights into evolution of spinescence and floral traits

Schinus, best known by its few cultivated and invasive species, is the largest genus of Anacardiaceae in southern South America. It is remarkably diverse compared to closely related genera, with approximately 42 species, most of which occur in several arid vegetation types and extend into Andean and Atlantic moist forests. The most comprehensive taxonomic revision of the genus dates to 1957, recognizing S. subg. Schinus and S. subg. Duvaua, the latter of which were further divided into two sections. Subsequent studies have highlighted morphological inconsistencies in this infrageneric classification, and species delimitation remains a challenge. Schinus has been poorly sampled in previous phylogenetic studies of Anacardiaceae, and thus any assumptions about its monophyly and relationships remain untested. We investigated the phylogenetic relationships of 44 Schinus taxa and sampled 122 specimens, including the outgroup, using nine nuclear and two plastid DNA sequence regions, most of them developed recently for Commiphora (Burseraceae, sister to Anacardiaceae). We used maximum parsimony, maximum likelihood, and Bayesian inference to infer relationships among species. We also constructed a morphological dataset, including vegetative anatomical features, and compared these characters to hypotheses based on molecular evidence in order to achieve a better understanding of the relationships among the species of Schinus and to related genera, aiming also to identify morphological characters and putative synapomorphies for major clades, and to discuss hypotheses regarding the evolution of structural traits in the genus. Our analyses strongly support the monophyly of Schinus, but also indicate that S. subg. Schinus and the sections of S. subg. Duvaua are polyphyletic. The phylogenetic relationships that emerged from our analyses include eight relatively well-supported lineages, but relationships among closely related species remain unclear in some clades. Ancestral state reconstructions demonstrate that several morphological and leaf-anatomical characters are valuable in characterizing some lineages. By contrast, most of the traits that have traditionally been used to circumscribe groups in Schinus show high levels of homoplasy. In light of these results, we present a novel sectional classification of Schinus based on a combination of character states associated with geographic distribution, corresponding to lineages that are mostly allopatric or at least ecologically distinct.

Fruit Morphology and Anatomy of the Spondioid Anacardiaceae

The Spondioideae subfamily of the Anacardiaceae is widely distributed today in tropical regions. Recent molecular phylogenetic investigations indicate that the Spondioideae are not monophyletic, but rather comprise at least two separate clades that are difficult to distinguish using vegetative and floral characters. Nevertheless, the syndrome of fruit characters traditionally used in identifying the subfamily is useful in discriminating genera of these clades and for identification of both modern and fossil anacardiaceous fruits. Here we document the morphology and anatomy of endocarps for representatives of all extant genera traditionally treated as Spondioideae, plus two genera that have been placed close to them in molecular investigations, Buchanania and Campnosperma. All genera are characterized by drupe-like fruits with sclerified stones that vary from uni- to multilocular depending on the genus. Germination modes vary throughout the Spondioideae. Some have characteristic plug-like opercula; others have recessed bilabiate germination valves, and still others open by apical flaps or simple slits. Although most currently recognized genera appear to be monophyletic, fruit morphology indicates that current circumscriptions of Cyrtocarpa, Poupartia and Tapirira are in need of revision.

Plastome Sequencing of Ten Nonmodel Crop Species Uncovers a Large Insertion of Mitochondrial DNA in Cashew

In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene and intron content, inversions, and expansion and contraction of the inverted repeat (IR). We identified a putative in cinnamon ( J. Presl) and other sequenced Lauraceae and an apparent functional transfer of to the nucleus of quinoa ( Willd.). In the orchard tree cashew ( L.), we report the insertion of an ∼6.7-kb fragment of mitochondrial DNA into the plastome IR. BLASTn analyses returned high identity hits to mitogenome sequences including an intact open reading frame. Using three plastome markers for five species of , we generated a phylogeny to investigate the distribution and timing of the insertion. Four species share the insertion, suggesting that this event occurred <20 million yr ago in a single clade in the genus. Our study extends the observation of mitochondrial to plastome IGT to include long-lived tree species. While previous studies have suggested possible mechanisms facilitating IGT to the plastome, more examples of this phenomenon, along with more complete mitogenome sequences, will be required before a common, or variable, mechanism can be elucidated.

Optimization of DNA extraction and PCR protocols for phylogenetic analysis in Schinopsis spp. and related Anacardiaceae

The Anacardiaceae is an important and worldwide distributed family of ecological and socio-economic relevance. Notwithstanding that, molecular studies in this family are scarce and problematic because of the particularly high concentration of secondary metabolites—i.e. tannins and oleoresins—that are present in almost all tissues of the many members of the group, which complicate the purification and amplification of the DNA. The objective of this work was to improve an available DNA isolation method for Schinopsis spp. and other related Anacardiaceae, as well as the PCR protocols for DNA amplification of the chloroplast trnL-F, rps16 and ndhF and nuclear ITS–ETS fragments. The modifications proposed allowed the extraction of 70–120 µg of non-degraded genomic DNA per gram of dry tissue that resulted useful for PCR amplification. PCR reactions produced the expected fragments that could be directly sequenced. Sequence analyses of amplicons showed similarity with the corresponding Schinopsis accessions available at GenBank. The methodology presented here can be routinely applied for molecular studies of the group aimed to clarify not only aspects on the molecular biology but also the taxonomy and phylogeny of this fascinating group of vascular plants.

An expanded nuclear phylogenomic PCR toolkit for Sapindales

PREMISE OF THE STUDY

We tested PCR amplification of 91 low-copy nuclear gene loci in taxa from Sapindales using primers developed for Bursera simaruba (Burseraceae).

METHODS AND RESULTS

Cross-amplification of these markers among 10 taxa tested was related to their phylogenetic distance from B. simaruba. On average, each Sapindalean taxon yielded product for 53 gene regions (range: 16-90). Arabidopsis thaliana (Brassicales), by contrast, yielded product for two. Single representatives of Anacardiaceae and Rutacaeae yielded 34 and 26 products, respectively. Twenty-six primer pairs worked for all Burseraceae species tested if highly divergent Aucoumea klaineana is excluded, and eight of these amplified product in every Sapindalean taxon.

CONCLUSIONS

Our study demonstrates that customized primers for Bursera can amplify product in a range of Sapindalean taxa. This collection of primer pairs, therefore, is a valuable addition to the toolkit for nuclear phylogenomic analyses of Sapindales and warrants further investigation.

Spiny plants, mammal browsers, and the origin of African savannas

Savannas first began to spread across Africa during the Miocene. A major hypothesis for explaining this vegetation change is the increase in C4 grasses, promoting fire. We investigated whether mammals could also have contributed to savanna expansion by using spinescence as a marker of mammal herbivory. Looking at the present distribution of 1,852 tree species, we established that spinescence is mainly associated with two functional types of mammals: large browsers and medium-sized mixed feeders. Using a dated phylogeny for the same tree species, we found that spinescence evolved at least 55 times. The diversification of spiny plants occurred long after the evolution of Afrotherian proboscideans and hyracoids. However, it is remarkably congruent with diversification of bovids, the lineage including the antelope that predominantly browse these plants today. Our findings suggest that herbivore-adapted savannas evolved several million years before fire-maintained savannas and probably, in different environmental conditions. Spiny savannas with abundant mammal herbivores occur in drier climates and on nutrient-rich soils, whereas fire-maintained savannas occur in wetter climates on nutrient-poor soils.

Unraveling the biogeographical history of Chrysobalanaceae from plastid genomes

PREMISE OF THE STUDY

The complex geological and climatic history of the Neotropics has had major implications on the diversification of plant lineages. Chrysobalanaceae is a pantropical family of trees and shrubs with 75% of its 531 species found in the Neotropics, and a time-calibrated phylogeny of this family should shed light on the tempo of diversification in the Neotropical flora. Previously published phylogenetic hypotheses of this family were poorly supported, and its biogeography remains unclear.

METHODS

We assembled the complete plastid genome of 51 Chrysobalanaceae species, and increased taxon sampling by Sanger-sequencing of five plastid regions for an additional 88 species. We generated a time-calibrated tree including all 139 Chrsyobalanaceae species and 23 outgroups. We then conducted an ancestral area reconstruction analysis and estimated diversification rates in the family.

KEY RESULTS

The tree generated with the plastid genome alignment was almost fully resolved. It supports the polyphyly of Licania and Hirtella. The family has diversified starting around the Eocene-Oligocene transition. An ancestral area reconstruction confirms a Paleotropical origin for Chrysobalanaceae with several transoceanic dispersal events. The main Neotropical clade likely resulted from a single migration event from Africa around 28 mya ago, which subsequently underwent rapid diversification.

CONCLUSIONS

Given the diverse ecologies exhibited by extant species, we hypothesize that the rapid diversification of Chrysobalanaceae following the colonization of the Neotropics was triggered by habitat specialization during the complex geological and paleoclimatic history of the Neotropics.

A Factor Graph Approach to Automated GO Annotation

As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum.

A revision of Spondias L. (Anacardiaceae) in the Neotropics

As part of an ongoing study of Anacardiaceae subfamily Spondioideae, the ten native and one introduced species of Spondias in the Neotropics are revised. The genus is circumscribed. Three new species, Spondiasadmirabilis, Spondiasexpeditionaria, and Spondiasglobosa, are described and illustrated; a key to the taxa found in the Neotropics and distribution maps are provided. The Paleotropical species and allied genera are reviewed. Diagnostic character sets include leaf architecture, habit, flower morphology, and gross fruit morphology. Notes on the ecology and economic botany of the species are provided.