Peter C. Hoch’s research while affiliated with Missouri Botanical Garden and other places

Previous systematic studies have generated abundant information on plants in family Onagraceae Juss., making this taxonomic group a model for understanding plant evolution. The chloroplast genome is widely used to provide valuable insights into how plant lineages evolved. In the present study, we employed shotgun sequencing to assemble new plastomes from Onagraceae. Plastomes of ten species and one genus, Fuchsia, are reported for the first time. We characterize and compare the plastome features of six genera (Chamaenerion, Circaea, Epilobium, Fuchsia, Ludwigia, and Oenothera), allowing us to reconstruct their phylogenies and explore inter- and infra-generic evolutionary relationships, inverted repeat (IR) expansion, plastome size increases, and correlations among repeat elements, genetic variations, and evolutionary events. Our findings indicate that each of the tribes and subfamilies we assessed exhibits unique plastome features. Our phylogenetic tree supports previous findings, but also reveals that some clades need further systematic analyses. We show that increased plastome size within subfamily Onagroideae coincides with IR expansion, which is not the case for subfamily Ludwigioideae. In addition, our results indicate that higher repeat numbers and greater genetic variation can serve as indicators of evolutionary events, such as gene loss and gain, IR boundary shifts, and inversions, but they may not have arisen universally across all members of Onagraceae. Our study provides some novel insights into plastome evolution in the Onagraceae. Further studies should aim to elucidate how plastome size has evolved in Ludwigioideae and explore the evolutionary roles of regions in Onagraceae plastomes exhibiting high repeat numbers and genetic variations.

Changes to flowering phenology are a key response of plants to climate change. However, we know little about how these changes alter temporal patterns of reproductive overlap (i.e. phenological reassembly). We combined long‐term field (1937–2012) and herbarium records (1850–2017) of 68 species in a flowering plant community in central North America and used a novel application of Bayesian quantile regression to estimate changes to flowering season length, altered richness and composition of co‐flowering assemblages, and whether phenological shifts exhibit seasonal trends. Across the past century, phenological shifts increased species' flowering durations by 11.5 d on average, which resulted in 94% of species experiencing greater flowering overlap at the community level. Increases to co‐flowering were particularly pronounced in autumn, driven by a greater tendency of late season species to shift the ending of flowering later and to increase flowering duration. Our results demonstrate that species‐level phenological shifts can result in considerable phenological reassembly and highlight changes to flowering duration as a prominent, yet underappreciated, effect of climate change. The emergence of an autumn co‐flowering mode emphasizes that these effects may be season‐dependent.

Background The evening primrose family (Onagraceae) includes 664 species (803 taxa) with a center of diversity in the Americas, especially western North America. Ongoing research in Onagraceae includes exploring striking variation in floral morphology, scent composition, and breeding system, as well as the role of these traits in driving diversity among plants and their interacting pollinators and herbivores. However, these efforts are limited by the lack of a comprehensive, well-resolved phylogeny. Previous phylogenetic studies based on a few loci strongly support the monophyly of the family and the sister relationship of the two largest tribes but fail to resolve several key relationships. Results We used a target enrichment approach to reconstruct the phylogeny of Onagraceae using 303 highly conserved, low-copy nuclear loci. We present a phylogeny for Onagraceae with 169 individuals representing 152 taxa sampled across the family, including extensive sampling within the largest tribe, Onagreae. Deep splits within the family are strongly supported, whereas relationships among closely related genera and species are characterized by extensive conflict among individual gene trees. Conclusions This phylogenetic resource will augment current research projects focused throughout the family in genomics, ecology, coevolutionary dynamics, biogeography, and the evolution of characters driving diversification in the family.

Background: While polyploids are common in plants, the evolutionary history and natural dynamics of most polyploid groups are still unclear. Owing to plentiful earlier systematic studies, Ludwigia sect. Isnardia (comprising 22 wetland taxa) is an ideal allopolyploid complex to investigate polyploid evolution and natural dynamics within and among taxa. With a considerable sampling, we concentrated on revisiting earlier phylogenies of Isnardia, reevaluating the earlier estimated age of the most recent common ancestor (TMRCA), exploring the correlation between infraspecific genetic diversity and ploidy levels, and inspecting interspecific gene flows among taxa. Results: Phylogenetic trees and network concurred with earlier phylogenies and hypothesized genomes by incorporating 192 atpB-rbcL and ITS sequences representing 91% of Isnardia taxa. Moreover, we detected three multi-origin taxa. Our findings on L. repens and L. sphaerocarpa were consistent with earlier studies; L. arcuata was reported as a multi-origin taxon here, and an additional evolutionary scenario of L. sphaerocarpa was uncovered, both for the first time. Furthermore, estimated Isnardia TMRCA ages based on our data (5.9 or 8.9 million years ago) are in accordance with earlier estimates, although younger than fossil dates (Middle Miocene). Surprisingly, infraspecific genetic variations of Isnardia taxa did not increase with ploidy levels as anticipated from many other polyploid groups. In addition, the exuberant, low, and asymmetrical gene flows among Isnardia taxa indicated that the reproductive barriers may be weakened owing to allopolyploidization, which has rarely been reported. Conclusions: The present research gives new perceptions of the reticulate evolution and dynamic nature of Isnardia and points to gaps in current knowledge about allopolyploid evolution.

https://twsps.wordpress.com/category/2023%e5%b9%b4%e6%9c%83%e6%9a%a8%e7%a0%94%e8%a8%8e%e6%9c%83/ Earlier systematic studies have accumulated abundant knowledge of Onagraceae plants, making this family a model group for understanding plant evolution. In the present study, we applied next-generation sequencing techniques and comparative analyses to give new perceptions on Onagraceae evolution. Totally, 12 newly assembled and 17 published plastomes representing six genera in Onagraceae were analyzed. Onagraceae plastomes are ca. 159,942 bp in length and contain 132-137 genes. Gene arrangement in Onagraceae is conserved except for some Oenothera taxa, while gene numbers, region sizes and boundaries, and nucleotide variations vary among genera. Moreover, most repeats are located in LSC as in many other plant groups. Onagraceae is similar to Lythraceae in the relative synonymous codon usage. In addition, our phylogeny mainly agrees with earlier research but suggests that Epilobium amurense and clades B3 and B4 in Ludwigia need further systematic studies.

Evolutionary shifts in breeding system are thought to have played key roles in the diversification of many lineages of plants, including the evening primrose family (Onagraceae), which includes the genus Oenothera L. Diversification in Oenothera has been accompanied by frequent breeding system shifts, but it is not clear whether these differences are due to shared evolutionary history or reflect repeated independent adaptations to varying ecological conditions. In this study, we focus on “Subclade B,” one of two primary clades within Oenothera, and combine phylogenetic reconstructions and breeding system data to evaluate evidence for multiple transitions to self-compatibility. This study includes 46 of the 58 named taxa (species and subspecies) of Oenothera Subclade B. Some taxa were sequenced in earlier analyses, available from GenBank, one was resampled here to add new sequences, and 28 taxa are newly sequenced here. We base our phylogeny on sequencing of portions of four chloroplast markers (rps16, ndhF, trnL-F, and rbcL) and two nuclear genes (ITS and ETS). We used pollination tests to verify or determine the breeding system of these taxa. Our phylogeny supports the current classification of Oenothera with minor changes and provides greater insight and clarity to the relationships of these species. Our results provide support for the monophyly of most of the sections in Oenothera Subclade B, as well as greater resolution for topology within sections Gaura (L.) W. L. Wagner & Hoch, Hartmannia (Spach) Walpers, Kneiffia (Spach) Walpers, and Megapterium (Spach) Walpers. Relationships among these monophyletic lineages, and the placement of sections Paradoxus W. L. Wagner and Peniophyllum (Pennell) Munz, and of the allopolypoid O. hispida (Benth.) W. L. Wagner, Hoch & Zarucchi, are not uniformly well-supported and need further clarification, but these phylogenetic uncertainties had minimal impact on the inference of transitions in self-compatibility in Subclade B. We use maximum likelihood, Bayesian inference and stochastic character mapping to estimate the minimum and maximum number of transitions necessary to explain the phylogenetic distribution of self-compatible lineages. Our results confirm at least 12 and possibly up to 15 independent transitions from self-incompatibility to self-compatibility in Oenothera Subclade B. This lability in breeding system, which is also seen broadly across Oenothera, lends strong support to the hypothesis that this trait plays a key role in the diversification of the genus.

Epilobium ravenii Hoch & Gandhi is proposed here as the new name for the species previously known as E. foliosum (Nutt. ex Torr. & A. Gray) Suksd., non E. foliosum Heynh.

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.

Biologists unable to recognize common plants, and a decline in botany students, faculty, courses, university departments, and herbaria, highlight the current erosion of botany. How did we reach this crisis, knowing that plants form the basis for life? What are the causes? What can we do to reverse it?

New Guinea is the world’s largest tropical island and has fascinated naturalists for centuries. Home to some of the best-preserved ecosystems on the planet and to intact ecological gradients—from mangroves to tropical alpine grasslands—that are unmatched in the Asia-Pacific region, it is a globally recognized centre of biological and cultural diversity. So far, however, there has been no attempt to critically catalogue the entire vascular plant diversity of New Guinea. Here we present the first, to our knowledge, expert-verified checklist of the vascular plants of mainland New Guinea and surrounding islands. Our publicly available checklist includes 13,634 species (68% endemic), 1,742 genera and 264 families—suggesting that New Guinea is the most floristically diverse island in the world. Expert knowledge is essential for building checklists in the digital era: reliance on online taxonomic resources alone would have inflated species counts by 22%. Species discovery shows no sign of levelling off, and we discuss steps to accelerate botanical research in the ‘Last Unknown’.