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

Abstract

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.

Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae)

“…Moreover, our results demonstrate that plastome data does not accurately reflect species relationships and is insufficient to resolve shallow level relationships within a rapidly radiated genus like Isodon . To achieve for a better resolved phylogeny of the genus, significant larger data sets derived from nuclear genome with next-generation sequencing technology might be helpful, such as targeted enrichment ( Gardner et al, 2020 ; Reichelt et al, 2021 ; Giaretta et al, 2022 ), deep genome skimming ( Liu et al, 2021 ), and RNA-seq ( Nevado et al, 2016 ; Jin et al, 2021 ; Kong et al, 2022 ; Xia et al, 2022 ), which are compatible with more comprehensive tools for disambiguating genetic lineages and causes of gene tree conflicts.…”

An updated classification for the hyper‐diverse genusCorydalis(Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence

“…Plastomes have been shown to be powerful tools for exploring phylogenetic relationships and resolving uncertain relationships at different taxonomic levels (Xu et al, 2019; Zhang et al, 2019; Li et al, 2021; Xu et al, 2022). The Angiosperms353 gene set (AGS), consisting of a set of 353 universal low‐copy nuclear genes, is increasingly being applied to infer the phylogenetic relationships of different lineages of angiosperms at multiple taxonomic scales (Johnson et al, 2019; Baker et al, 2022; Gagnon et al, 2022; Giaretta et al, 2022; Kandziora et al, 2022; Simoes et al, 2022; Zhou et al, 2022). Target sequence capture is an efficient and cost‐effective method for obtaining DNA sequence data from genome skimming data for phylogeny reconstruction (Liu et al, 2021).…”

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

“…Analysis of closely related lineages in a subset is likely to incorporate less genealogical discordance and avoid genuine phylogenetic signal being blurred by stochastic processes such as gene duplication and loss, hybridization, and incomplete lineage sorting (see Smith et al, 2015; Molloy and Warnow, 2018). In Eugenia , a more data rich sample obtained from targeted sequencing recognized that conflicting signal are involved in the low support recurrently recovered along the backbone (Giaretta et al, 2022), which suggests that incomplete lineage sorting or other stochastic processes may play a role in Myrteae phylogenetics. Rapid radiation and recent divergence have been implicated in phylogenetic incongruence and incomplete lineage sorting (Cai et al, 2021; Meleshko et al, 2021) and further studies will be able to determine if this is also the case in Myrteae.…”

“…This method will also open the opportunity of contrasting complementary datasets to best assess deep and shallow phylogenetic levels as well as perform relevant genomic analyses to recognize if other processes than genuine conflict signals are taking place. For instance, Giaretta et al (2022) yielded several infrageneric level topologies of Eugenia contrasting different datasets (exons, introns and off-target plastid) and reconstructions methods based on the Angiosperms-353. Even though their general topology agrees with the previous phylogenetic reconstructions (e.g.…”