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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. [ABSTRACT FROM AUTHOR]

• The pericarp anatomy of Eugeniinae species revealed Myrcianthes pungens (which is in the genus sister to Eugenia) has a drupe-like fruit. • In species of Eugeniinae, the dorsal and ventral meristems in the ovary wall give rise to a mesocarp with three distinct regions. • This work supports the importance of ontogenic studies to appropriately delimit pericarp layers and may help reveal patterns in the pericarp structure that can contribute to estimating phylogenetic relationships. The genus Eugenia is of great ecological importance and due to being very diverse has been the subject of a comprehensive phylogenetic and taxonomic review to create an accurate classification. This study sought to describe the pericarp ontogeny of species in the subtribe Eugeniinae to reveal anatomical features that can be used to characterize morphologically similar sections. Buds, flowers, and fruits were collected at different development stages from herbarium specimens and plants in the field. Herbarium material underwent a reversal procedure, and fresh material was submitted to conventional anatomical analysis techniques and evaluated under an optical light microscope. By analyzing the species, we verified some promising characteristics, such as the following: a drupe-like fruit in Myrcianthes pungens (which is in the genus sister to Eugenia) that is a novelty for this species; trichomes in the inner epidermis of the ovary in species in Eugenia sect. Hexachlamys and E. sect. Pilothecium ; and the absence of intercellular spaces in the most internal layers of the mesocarp in a species of E. section Speciosae. Representatives from the subtribe showed predominant cell division in the layers subjacent to the exocarp (dorsal meristem) and endocarp (ventral meristem) and the outer, middle and inner mesocarp. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]