Flora of the World

The delimitation of species boundaries has been a constant challenge to the fields of systematics, natural history, and conservation biology. Subtle and minor morphological differences in a widespread species complex make delimiting species boundaries particularly difficult. High throughput targeted sequencing of hundreds of loci has allowed researchers to obtain improved insights into evolutionary processes and resolved previously ambiguous phylogenetic relationships. Piper amalago (subgenus Gonistum) is morphologically similar to, and geographically overlaps with, many other Neotropical Piper species that have narrow restricted distributions, or occur as narrow endemics. Taxonomists have debated whether morphological differences between P. amalago and other similar species merit distinct species status or if these taxa represent a single widespread species exhibiting extensive intraspecific variation. Recent molecular analyses demonstrated that P. amalago is paraphyletic with morphologically similar species, notably P. martensianum, but these findings lack phylogenetic support. This study investigates the phylogenetic relationships of P. amalago and several closely related species using multiple DNA sequences, and seeks to determine whether species can be delimited on the basis of phylogenetic, geographical, and morphological information. The Angiosperms353 bait set was used to retrieve nuclear genes to build maximum likelihood and multispecies coalescent phylogenetic hypotheses. Available DNA sequence data are consistent with the presence of a single, monophyletic, widespread species complex, with considerable morphological variation and some geographic structure. While the drivers of the morphological variation within this complex are not yet fully understood, we have a better understanding of evolutionary relationships and species boundaries within Piper, a giant genus.

DOI:

10.1016/j.ympev.2025.108457

View Publication

A piece of the Piper puzzle: Systematics of Piper section Enckea, a Neotropical section in a giant genus

Cara Hastings, Emma Casselman, Christopher Davidson,

Systematic Botany

2024

Vol. 49, Issue 3

pp. 547-566

Piper (Piperaceae) is a species-rich pantropical genus (∼2000 species) with distinctive morphological characteristics such as swollen nodes, lack of a perianth, and one-seeded berry fruits. Sub-generic lineages within Piper are often associated with morphological traits and are well supported with molecular data, but sampling in previous studies was incomplete and conflict exists between morphological data and molecular inference. In this paper, Piper section Enckea is evaluated for monophyly by pairing DNA, primarily from herbarium material, with the Angiosperms353 bait set, high throughput sequencing, recently developed bioinformatic techniques, and two methods of phylogenetic reconstruction, maximum likelihood and multi-species coalescence. The results suggest continued support for recognition of Piper sect. Enckea as a monophyletic section and contribute to a better understanding of relationships among species within the section. However, they also raise questions about the morphological features used to define P. sect. Enckea and delimit species within the section.

DOI:

10.1600/036364424x17267811220452

View Publication

Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae)

Sara E. Simmonds, James F. Smith, Christopher Davidson,

Molecular Phylogenetics and Evolution

2021

Vol. 163

pp. 107229

Abstract

Biological radiations provide unique opportunities to understand the evolution of biodiversity. One such radiation is the pepper plant family Piperaceae, an early-diverging and mega-diverse lineage that could serve as a model to study the diversification of angiosperms. However, traditional genetic markers lack sufficient variation for such studies, and testing hypotheses on poorly resolved phylogenetic frameworks becomes challenging. Limited genomic data is available for Piperaceae, which contains two of the largest genera of angiosperms, Piper (>2100 species) and Peperomia (>1300 species). To address this gap, we used genome skimming to assemble and annotate whole plastomes (152–161kbp) and >5kbp nuclear ribosomal DNA region from representatives of Piper and Peperomia. We conducted phylogenetic and comparative genomic analyses to study plastome evolution and investigate the role of hybridization in this group. Plastome phylogenetic trees were well resolved and highly supported, with a hard incongruence observed between plastome and nuclear phylogenetic trees suggesting hybridization in Piper. While all plastomes of Piper and Peperomia had the same gene content and order, there were informative structural differences between them. First, ycf1 was more variable and longer in Piper than Peperomia, extending well into the small single copy region by thousands of base pairs. We also discovered previously unknown structural variation in 14 out of 25 Piper taxa, tandem duplication of the trnH-GUG gene resulting in an expanded large single copy region. Other early-diverging angiosperms have a duplicated trnH-GUG, but the specific rearrangement we found is unique to Piper and serves to refine knowledge of relationships among early-diverging angiosperms. Our study demonstrates that genome skimming is an efficient approach to produce plastome assemblies for comparative genomics and robust phylogenies of species-rich plant genera.

DOI:

10.1016/j.ympev.2021.107229

View Publication

The emergence of earliest angiosperms may be earlier than fossil evidence indicates

Karsten Salomo, James F. Smith, Taylor S. Feild,

Systematic Botany

2017

Vol. 42, Issue 4

pp. 607-619

Gaps between molecular ages and fossils undermine the validity of time-calibrated molecular phylogenies. An example of the time gap surrounds the age of angiosperms’ origin. We calculate molecular ages of the earliest flowering plant lineages using 22 fossil calibrations (101 genera, 40 families). Our results reveal the origin of angiosperms at the late Permian, ∼275 million years ago. Different prior probability curves of molecular age calculations on dense calibration point distributions had little effect on overall age estimates compared to the effects of altered calibration points. The same is true for reasonable root age constraints. We conclude that our age estimates based on multiple datasets, priors, and calibration points are robust and the true ages are likely between our extremes. Our results, when integrated with the ecophysiological evolution of early angiosperms, imply that the ecology of the earliest angiosperms is critical to understand the pre-Cretaceous evolution of flowering plants.

DOI:

10.1600/036364417x696438

View Publication

A new endemic species of Trigonachras (Sapindaceae) from Sabah, Malaysia (Borneo)

Sven Buerki, Christopher Davidson, Joan T. Pereira,

Phytotaxa

2013

Vol. 88, Issue 2

pp. 19

A new species of Trigonachras from Borneo is described and illustrated. Trigonachras postardanjeisin is endemic to the ultramafic soils of the Tawai Forest Reserve in Sabah, Malaysia (Borneo). It is morphologically close to the widespread Trigonachras acuta but differs by its glabrous inflorescence and infrutescence axes and fruits. The two species also differ by their ecology and distribution. Line drawings are provided for the new taxa, along with discussions of its morphological affinities and preliminary risk of extinction assessment.

DOI:

10.11646/phytotaxa.88.2.1

View Publication