Mark Chase

Royal Botanic Gardens, Kew · Science

Over the last 6 million years, the arid Australian Eremaean Zone (EZ) has remained as dry as it is today. A widely accepted hypothesis suggests that the flora and fauna of arid regions were more broadly distributed before aridification began. In Australia, this process started around 20 million years ago (Ma), leading to gradual speciation as the c...

Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited, with diversity assessments often relying on only a few samples or DNA markers. Here we employed restriction-site associated DNA sequencing to analyze 175 P. nigrum accessions from ei...

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundation...

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up‐to‐date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high‐throughput and Sanger sequencing data, covering all five s...

Orchids constitute one of the most spectacular radiations of flowering plants. However, their geographical origin, historical spread across the globe, and hotspots of speciation remain uncertain due to the lack of a broad phylogenomic framework. ⍰ We present a new Orchidaceae phylogeny based on high-throughput and Sanger sequencing datasets, coveri...

Nine new species in Australian Nicotiana section Suaveolentes are described, including N. clarksonii M.W.Chase & Christenh., N. erytheia M.W.Chase & Christenh., N. latifolia M.W.Chase & Christenh., N. latzii M.W.Chase, R.W.Jobson & Christenh., N. gibbosa M.W.Chase, D.D.Andrew & J.J.Bruhl, N. olens M.W.Chase & Christenh., N. praecipitis M.W.Chase &...

Gastrodia Brown (1810: 330) is a genus of leafless olomycotrophic terrestrial orchids comprising around 94 species (including one natural hybrid) widely distributed from tropical Africa through Japan and the Australasian region (Govaerts et al. 2022). It is characterized by fleshy underground tuber, a smooth or coralloid rhizome, a perianth tube fo...

Neotropical Maranta has repeatedly emerged as non-monophyletic in molecular phylogenetic studies, but no taxonomic changes have been proposed due to previous weak support for the main clades and overall sparse taxonomic sampling. Our study includes a phylogenetic hypothesis strictly based on molecular evidence, using nuclear ribosomal (nrITS) and p...

Although some authors previously questioned the circumscription of Nicotiana benthamiana, it has never been treated taxonomically as more than a single widespread, variable species. A recent study employing phylogenetic and population genetic analyses has demonstrated that N. benthamiana comprises five species that are geographically and morphologi...

To provide insights into the fate of transposable elements (TEs) across timescales in a post-polyploidization context, we comparatively investigate five sibling Dactylorhiza allotetraploids (Orchidaceae) formed independently and sequentially between 500 and 100K generations ago by unidirectional hybridisation between diploids D. fuchsii and D. inca...

One of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. T...

The Epidendrum nocturnum Jacq. group comprises about 60 species. Nine species occur in Brazil, predominantly in the Atlantic and Amazon Forests. The group is taxonomically complex because its species are morphologically similar and not easily distinguished. The main objective of this work is to characterize their chromosome evolution and how this h...

We present a phylogenetic analysis using plastid (matK, rbcL) and nuclear (nrITS) DNA for diverse Euploca spp. (formerly Heliotropium section Orthostachys) from the worldwide distribution of a genus and including species encompassing the wide physiological and morphological diversity of the genus. Our results indicate that some remarkably complex f...

One of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. H...

Background and aims: The extent to which genome size and chromosome numbers evolve in concert is little understood, particularly after polyploidy (whole-genome duplication), when a genome returns to a diploid-like condition (diploidisation). We study this phenomenon in 46 species of allotetraploid Nicotiana section Suaveolentes (Solanaceae), which...

Some groups in Epidendrum have stable chromosome numbers, whereas the species of Epidendrum subgenus Amphiglottium exhibit high levels of chromosome number variability and other genomic alterations. Polyploidy and dysploidy have both been invoked to explain chromosome number variation in the subgenus, but little is known about what is driving the h...

Here we study a challenging group of karyotypically highly variable Epidendrum spp. using phylogenetic methods to help understand how hybridization/introgression contributes to karyotype evolution. We hypothesize that species with great chromosome number variation are a result of past hybridization/introgression. Conflicting topologies in trees con...

Background Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the mos...

We present the first comparative plastome study of Pleurothallidinae with analyses of structural and molecular characteristics and identification of the ten most-variable regions to be incorporated in future phylogenetic studies. We sequenced complete plastomes of eight species in the subtribe and compared phylogenetic results of these to parallel...

Nicotiana hesperis is illustrated from plants collected near the Billabong Roadhouse in north-western Western Australia, which were cultivated at the Royal Botanic Gardens, Kew. Its taxonomic history, ecology, cytology and cultivation are discussed.

The Australian species Nicotiana walpa is newly described here from plants collected at the Uluru-Kata Tjuta National Park in the Northern Territory, Australia, and illustrated from plants cultivated at the Royal Botanic Gardens, Kew. Its discovery, ecology, cytology and cultivation are discussed.

The new species Nicotiana pila is described here from plants collected in the Little Sandy Desert of Western Australia. Seeds were germinated and plants cultivated at the Royal Botanic Gardens, Kew, which were used for the illustration. Its taxonomic history, ecology, cytology and cultivation are discussed.

Nicotiana murchisonica is described here. It is illustrated from plants collected along the Murchison River and tributaries in Western Australia and cultivated at the Royal Botanic Gardens, Kew. Its discovery, ecology, cytology and cultivation are discussed.

In this volume of Curtis's Botanical Magazine, we increase the number of species recognised in Nicotiana sect. Suaveolentes to 38, up from the 21 recorded in the Flora of Australia published 39 years ago, but we estimate the final number is likely to exceed 60. We examine the reasons why so many unrecognised species exist. Several Australian and Am...

Nicotiana rosulata is illustrated from plants grown from seeds collected near Leonora in the Goldfields region of Western Australia. The plants were cultivated in the quarantine house of the Royal Botanic Gardens, Kew. The taxonomic history, ecology, cytology and cultivation of this species are discussed.

Nicotiana megalosiphon is illustrated from plants cultivated at the Royal Botanic Gardens, Kew, which were grown from seeds collected near the bridge over the Mehi River near Moree, New South Wales, Australia. Its taxonomic history, ecology, cytology, etymology and cultivation are discussed. The two subspecies previously recognised within this taxo...

The Australian species Nicotiana hoskingii from the Planchonella Nature Reserve in New South Wales is newly described and illustrated from plants cultivated at the Royal Botanic Gardens, Kew. Its discovery, ecology, cytology and cultivation are discussed.

Nicotiana monoschizocarpa is illustrated from plants collected along the banks of the Daly River in the Northern Territory (Australia) and cultivated at the Royal Botanic Gardens, Kew. Its taxonomic history, ecology, cytology and cultivation are discussed.

Nicotiana salina is described here and illustrated from plants collected at Weelhamby Lake, a salt lake in Western Australia, and cultivated at the Royal Botanic Gardens, Kew. We discuss its ecology and cultivation.

The new species Nicotiana insecticida, which is remarkable in its insect trapping abilities, is described here. It is illustrated from plants that were grown from seeds collected near the Minilya Roadhouse on the Northwest Coastal Highway in Western Australia, Australia. They were cultivated at the Royal Botanic Gardens, Kew. Its distinguishing fea...

Plants collected in Towarri National Park in New South Wales were cultivated at the Royal Botanic Gardens, Kew. It is illustrated here and described as the new species, Nicotiana notha. Its origin, cytology, taxonomic history, ecology and cultivation are discussed.

Nicotiana truncata is illustrated from plants collected between Coober Pedy and Oodnadatta in South Australia and cultivated at the Royal Botanic Gardens, Kew. Its taxonomic history, ecology, cytology and cultivation are discussed.

Nicotiana exigua is illustrated from plants collected in New South Wales, Australia, at the Narran Lake Nature Reserve and cultivated at the Royal Botanic Gardens, Kew. Its taxonomic history, ecology, cytology and cultivation are discussed.

Nicotiana ingulba is returned to species level here. It is illustrated from plants cultivated at the Royal Botanic Gardens, Kew, which were grown from seeds collected in the Uluru‐Kata Tjuta National Park in the Northern Territory, Australia. Its taxonomic history, ecology, cytology, etymology and cultivation are discussed.

To contribute to what is known about involvement of vegetation dynamics in Neotropical speciation, we used the Epidendrum latilabre complex, a taxonomically well-defined species group, to investigate past connections between Amazonian (AM) and Atlantic (AF) forests and address the following topics: (1) divergence times between sister species curren...

To contribute to what is known about involvement of vegetation dynamics in Neotropical speciation, we used the Epidendrum latilabre complex, a taxonomically well-defined species group, to investigate past connections between Amazonian (AM) and Atlantic (AF) forests and address the following topics: (1) divergence times between sister species curren...

Premise: The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the e...

Coelogyne has been shown in analyses of molecular data to be polyphyletic with 14 other genera of Coelogyninae (Arethuseae) embedded. Three possible solutions to establish an alternative classification are considered: lumping all of these in the oldest genus, in this case Coelogyne, distinguishing two genera corresponding to the two main clades in...

The jewel orchids (Goodyerinae), named after their often colourful leaves, have a pantropical distribution with a clear Asian centre of diversity. However, the Nearctic and Neotropical America together form a second centre of diversity, with one-third of known species of Goodyerinae. Previously, only a few American samples have been included in phy...

Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To addr...

Eulophia (Eulophiinae; Epidendroideae) has been found in molecular phylogenetic studies to be non-monophyletic. Here, we propose to combine it with Acrolophia, Cymbidiella, Eulophiella, Geodorum, Oeceoclades and Paralophia and discuss the characters that have been used previously to discriminate among these genera, demonstrating that none of them i...

Background and aims: Extant plant groups with a long fossil history are key elements in understanding vascular plant evolution. Horsetails (Equisetum, Equisetaceae) have a nearly continuous fossil record dating back to the Carboniferous, but their phylogenetic and biogeographic patterns are still poorly understood. We use here the most extensive p...

We explore the origins of the extraordinary plant diversity in the Qinghai-Tibetan Plateau (QTP) using Orchidinae (Orchidaceae) as a model. Our results indicate that six major clades in Orchidinae exhibited substantial variation in the temporal and spatial sequence of diversification. Our time-calibrated phylogenetic model suggests that the species...

We studied the evolutionary history of Chrysobalanaceae with phylogenetic analyses of complete plastid genomes from 156 species to assess the tempo of diversification in the Neotropics and help to unravel the causes of Amazonian plant diversification. These plastid genomes had a mean length of 162 204 base pairs, and the nearly complete DNA sequenc...

To address the polyphyly of Phaius and Calanthe in recent molecular studies, we recommend the merger of these genera along with Cephalantheropsis and Gastrorchis, which are embedded among the first two genera. Some authors have instead proposed to segregate new genera from both Phaius and Calanthe, but this results in generic concepts for which the...

Premise of the study Evolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to...

In this study, we analyse a species complex in Epidendrum, a mega-diverse Neotropical orchid genus, that is formed by the 11 Brazilian species of the E. difforme group. Although this group (c. 100 taxa) exhibits relatively high levels of floral variation, the Brazilian species are similar, making delimitation problematic. Here we combine molecular...

In this study, we analyse a species complex in Epidendrum, a mega-diverse Neotropical orchid genus, that is formed by the 11 Brazilian species of the E. difforme group. Although this group (c. 100 taxa) exhibits relatively high levels of floral variation, the Brazilian species are similar, making delimitation problematic. Here we combine molecular...

New combinations and names are proposed for species formerly placed in three genera of subtribe Bletiinae. Based on the latest phylogenetic analyses of the subtribe in which species of Basiphyllaea and Hexalectris were embedded among the species of Bletia, twelve new combinations and a new name are proposed in the last.

Nicotiana section Suaveolentes is the largest section of Nicotiana and is a monophyletic group of allotetraploid species. Most of the species are endemic to Australia, but three species occur on islands in the South Pacific as far east as French Polynesia and one species is native to Namibia. Here, we present phylogenetic results based on genome sk...

Pantropical Bulbophyllum, with ∼2,200 species, is one of the largest genera in Orchidaceae. Although phylogenetics and taxonomy of the ∼60 American species in the genus are generally well understood, some species complexes need more study to clearly delimit their component species and provide information about their evolutionary history. Previous r...

Tiganophyton karasense, an evergreen dwarf shrub, is described as a new species. A new genus and family are also proposed for it in the order Brassicales. Phylogenetic analysis of DNA sequence data indicate that Tiganophyton is sister to Bataceae/Salvadoraceae, and all three sister to Koeberliniaceae. First realized to be undescribed in 2010, T. ka...

Nicotiana section Suaveolentes is the largest section of Nicotiana and is a monophyletic group of allotetraploid species. Most of the species are endemic to Australia, but three species occur on islands in the South Pacific as far east as French Polynesia and one species is native to Namibia. Here, we present phylogenetic results based on genome sk...

Many new combinations are needed in Euploca, previously regarded as Heliotropium section Orthostachys, to correspond with results of our forthcoming, world-wide, molecular phylogenetic analysis. We also need these names for our many δ13C determinations that identify many Euploca species exhibiting C4 photosynthesis and show that other Euploca speci...

Allopolyploidy is acknowledged as an important force in plant evolution. Frequent allopolyploidy in Nicotiana across different timescales permits the evaluation of genome restructuring and repeat dynamics through time. Here we use a clustering approach on high-throughput sequence reads to identify the main classes of repetitive elements following t...

This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification of the most variable regions (hotspots) in this group of orchids. These structure of these six plastomes is relatively conserved, exhibiting lengths ranging between 142,599 to 154,562 bp with 36.7% GC on average and exhibiting ty...

Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situa...

Background: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to...

Background: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to...

Background: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to...

Cactaceae species are karyotypically well-known with x = 11 and chromosome number variation due mainly to polyploidization. However, both assumptions are based on descriptive observations without taking an evolutionary framework of Cactaceae into account. Aiming to confirm these hypotheses in an evolutionary context, we obtained chromosome numbers...

Background: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to...

Background Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to r...

Methods for RNA isolation These methods were originally included in Appendix S1 of "Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes" Marc T. J. Johnson et al. PLOS ONE, November 21, 2012. https://doi.org/10.1371/journal.pone.0050226 Many of the protocols share element...

This protocol is part of a collection of eighteen protocols used to isolate total RNA from plant tissue. (RNA Isolation from Plant Tissue Collection: https://www.protocols.io/view/rna-isolation-from-plant-tissue-439gyr6) and was originally published as part of Appendix S1 of "Evaluating Methods for Isolating Total RNA and Predicting the Success of...