A Foundational Population Genetics Investigation of the Sexual Systems of Solanum (Solanaceae) in the Australian Monsoon Tropics Suggests Dioecious Taxa May Benefit from Increased Genetic Admixture via Obligate Outcrossing.

Solanum section Leptostemonum is an ideal lineage to test the theoretical framework regarding proposed evolutionary benefits of outcrossing sexual systems in comparison to cosexuality. Theoretically, non-cosexual taxa should support more genetic diversity within populations, experience less inbreeding, and have less genetic structure due to a restricted ability to self-fertilize. However, many confounding factors present challenges for a confident inference that inherent differences in sexual systems influence observed genetic patterns among populations. This study provides a foundational baseline of the population genetics of several species of different sexual systems with the aim of generating hypotheses of any factor-including sexual system-that influences genetic patterns. Importantly, results indicate that dioecious S. asymmetriphyllum maintains less genetic structure and greater admixture among populations than cosexual S. raphiotes at the same three locations where they co-occur. This suggests that when certain conditions are met, the evolution of dioecy may have proceeded as a means to avoid genetic consequences of self-compatibility and may support hypotheses of benefits gained through differential resource allocation partitioned across sexes. Arguably, the most significant finding of this study is that all taxa are strongly inbred, possibly reflective of a shared response to recent climate shifts, such as the increased frequency and intensity of the region's fire regime.

Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants.

Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole-genome triplication (WGT1) at ∼81 million years ago (mya), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 mya. In addition, we detected two gene duplication bursts (GDBs) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families revealed that 21 gene clades have retained gene duplicates. These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.

Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum.

PREMISE: Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. METHODS: A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set). RESULTS: While the taxonomic framework of Solanum remained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths. The strongest area of discordance, near the crown node of Solanum, could potentially represent a hard polytomy. CONCLUSIONS: We argue that incomplete lineage sorting due to rapid diversification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages.

Solanumscalarium (Solanaceae), a newly-described dioecious bush tomato from Judbarra/Gregory National Park, Northern Territory, Australia.

A new species of functionally dioecious bush tomato of SolanumsubgenusLeptostemonum is described. Solanumscalarium Martine & T.M.Williams, sp. nov., is a member of the taxonomically challenging "Kimberley dioecious clade" in Australia and differs from other species in the group in its spreading decumbent habit and conspicuously prickly male floral rachis. The species is so far known from one site in Judbarra/Gregory National Park in the Northern Territory. Ex situ crosses and confirmation of inaperturate pollen grains produced in morphologically cosexual flowers indicate that these flowers are functionally female and the species is functionally dioecious. The scientific name reflects the ladder-like appearance of the inflorescence rachis armature of male individuals, the stone staircase that provides access to the type locality at the Escarpment Lookout Walk, and the importance of maintaining equitable and safe access to outdoor spaces. The common name Garrarnawun Bush Tomato is proposed in recognition of the lookout point at this site, a traditional meeting place of the Wardaman and Nungali-Ngaliwurru peoples whose lands overlap in this area.

Differential reward in "male" versus "female" pollen of functionally dioecious Solanum.

PREMISE: Five to six percent of angiosperm species exhibit a dioecious sexual system, with unisexual "male" or "female" flowers borne on separate plants. The consequent need for inter-individual pollen exchange is a special challenge for taxa where pollen is the sole pollinator reward. Dioecious Australian Solanum assure visits from pollen-foraging bees via production of inaperturate pollen in functionally female (morphologically bisexual) flowers. Biochemical composition of pollen from Australian Solanum has not been assessed nor compared to porate pollen from staminate flowers to reveal whether these flowers differ in their pollinator reward potential. METHODS: Porate pollen from male flowers and inaperturate pollen from functionally female flowers of two functionally dioecious Australian species were compared for protein and amino acid content. We also assessed pollen from bisexual and staminate flowers of a closely related andromonoecious species, in which all pollen is porate, as a comparison across co-occurring sexual systems. RESULTS: In both functionally dioecious species, porate pollen grains from staminate flowers had significantly higher levels of proteins and amino acids than inaperturate pollen grains from functionally female flowers. Levels of proteins and amino acids were highest in bisexual and staminate flowers of the andromonoecious species. CONCLUSIONS: Higher levels of proteins and amino acids in porate pollen of "male" flowers in our functionally dioecious Solanum species suggests a greater nutritive reward for bees foraging on "male" plants than for those foraging on functionally "female" plants. Greater reward in porate pollen (including andromonoecious species) may be connected to the potential to generate a pollen tube.

A basic ddRADseq two-enzyme protocol performs well with herbarium and silica-dried tissues across four genera.

PREMISE: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double-digest restriction site-associated DNA sequencing (ddRADseq) protocol using DNAs from four genera extracted from both silica-dried and herbarium tissue. METHODS: DNAs from Draba, Boechera, Solidago, and Ilex were processed with a ddRADseq protocol. The effects of DNA degradation, taxon, and specimen age were assessed. RESULTS: Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples. DISCUSSION: These results suggest that herbarium samples can be incorporated into ddRADseq project designs, and that specimen age can be used as a rapid on-site guide for sample choice. The detailed protocol we provide will allow users to pursue herbarium-based ddRADseq projects that minimize the expenses associated with fieldwork and sample evaluation.

Integrated pest management in the academic small greenhouse setting: A case study using Solanum spp. (Solanaceae).

PREMISE: Botanical faculty and staff at academic institutions are often tasked with establishing and/or caring for plant collections held in small greenhouse facilities. Once plants are in place, an especially acute challenge is managing plant pest/pathogen populations. Integrated pest management (IPM) approaches are an excellent option, but few examples exist in the literature of successful programs that have been developed in academic small greenhouse settings. METHODS AND RESULTS: Over several years, we developed an IPM program for two small research greenhouses on the campus of a primarily undergraduate institution where hundreds of plants have been grown for studies in the genus Solanum. We here present a synopsis of the cultural, mechanical, physical, and biological controls used as part of our successful IPM strategy-including details on the efficacy of multiple predatory insects-with the hope of providing a model for sustainable pest management in the higher education environment. CONCLUSIONS: IPM can be an effective strategy for maintaining healthy plant populations in small research greenhouses, but it requires a consistent investment of time and funding. A well-cared-for plant collection might help support numerous positive outcomes, including advances in faculty scholarship and opportunities for student learning and/or training.

Solanumplastisexum, an enigmatic new bush tomato from the Australian Monsoon Tropics exhibiting breeding system fluidity.

A bush tomato that has evaded classification by solanologists for decades has been identified and is described as a new species belonging to the Australian "Solanumdioicum group" of the Ord Victoria Plain biogeographic region in the monsoon tropics of the Northern Territory. Although now recognised to be andromonoecious, S.plastisexum Martine & McDonnell, sp. nov. exhibits multiple reproductive phenotypes, with solitary perfect flowers, a few staminate flowers or with cymes composed of a basal hermaphrodite and an extended rachis of several to many staminate flowers. When in fruit, the distal rachis may abcise and drop. A member of SolanumsubgenusLeptostemonum, Solanumplastisexum is allied to the S.eburneum Symon species group. Morphometric analyses presented here reveal that S.plastisexum differs statistically from all of its closest relatives including S.eburneum, S.diversiflorum F. Meull., S.jobsonii Martine, J.Cantley & L.M.Lacey, S.succosum A.R.Bean & Albr. and S.watneyi Martine & Frawley in both reproductive and vegetative characters. We present evidence supporting the recognition of S.plastisexum as a distinctive entity, a description of the species, representative photographs, a map showing the distribution of members of the S.eburneum species group and a key to the andromonoecious Solanum species of the Northern Territory of Australia. This new species is apparently labile in its reproductive expression, lending to its epithet, and is a model for the sort of sexual fluidity that is present throughout the plant kingdom.

Phylogeny of the Australian Solanum dioicum group using seven nuclear genes, with consideration of Symon's fruit and seed dispersal hypotheses.

The dioecious and andromonoecious Solanum taxa (the "S. dioicum group") of the Australian Monsoon Tropics have been the subject of phylogenetic and taxonomic study for decades, yet much of their basic biology is still unknown. This is especially true for plant-animal interactions, including the influence of fruit form and calyx morphology on seed dispersal. We combine field/greenhouse observations and specimen-based study with phylogenetic analysis of seven nuclear regions obtained via a microfluidic PCR-based enrichment strategy and high-throughput sequencing, and present the first species-tree hypothesis for the S. dioicum group. Our results suggest that epizoochorous trample burr seed dispersal (strongly linked to calyx accrescence) is far more common among Australian Solanum than previously thought and support the hypothesis that the combination of large fleshy fruits and endozoochorous dispersal represents a reversal in this study group. The general lack of direct evidence related to biotic dispersal (epizoochorous or endozoochorous) may be a function of declines and/or extinctions of vertebrate dispersers. Because of this, some taxa might now rely on secondary dispersal mechanisms (e.g. shakers, tumbleweeds, rafting) as a means to maintain current populations and establish new ones.

The hidden Heuchera: How science Twitter uncovered a globally imperiled species in Pennsylvania, USA.

The genus Heuchera is recognized as one of the most diverse endemic radiations of Saxifragaceae in North America, yet species delimitation and geographic distribution within the group remain controversial. Many species remain difficult to identify, including Heuchera alba, a narrow Appalachian endemic and globally imperiled (G2) taxon recorded only from West Virginia and Virginia that occurs in sympatry with H. pubescens and H. americana. A recent survey of the cliffside flora of the Shikellamy Bluffs, PA recorded dozens of Heuchera individuals that, through the use of social media, were positively identified as H. alba. Aided by examination of historical herbarium records, subsequent searches of similar habitats in Pennsylvania led to the discovery of seven more populations and established a significant range expansion for this rare species. The uncovering of H. alba in Pennsylvania is an exciting conservation outcome and an example of what can happen when botanists embrace a combination of modern and classical approaches to discovery and collaboration.

Solanum jobsonii, a novel andromonoecious bush tomato species from a new Australian national park.

A new species of Solanum from the Australian "andromonoecious bush tomato clade" of Solanum subgenus Leptostemonum is described. Solanum jobsonii Martine, J.Cantley, & L.M.Lacey, sp. nov. is part of the S. eburneum Symon species group. It most closely resembles S. eburneum and S. watneyi Martine & Frawley of the northwestern part of the Northern Territory, but is separated geographically from them by the Sturt Plateau. Morphometric analyses show that S. jobsonii differs statistically from S. eburneum, S. watneyi, and S. diversiflorum F.Muell. - a similar species in habit and leaf characters - in several key reproductive and vegetative characters. We provide morphometric evidence for the recognition of S. jobsonii, a complete description, a table of comparisons within its species group, and a map showing species group distributions. One of the first new species to be described from Limmen National Park (established 2012), S. jobsonii is a testament to the value of designating and protecting public lands, as well as supporting science relating to them.

Understory dominance and the new climax: Impacts of Japanese knotweed (Fallopia japonica) invasion on native plant diversity and recruitment in a riparian woodland.

Riparian forests exhibit levels of ecological disturbance that leave them especially prone to biological invasions. Japanese knotweed (Fallopia japonica) is particularly suited to these habitats and is an aggressive invader along watercourses throughout its now-global range as an exotic invader. Using one of the few Silver Maple Floodplain Forest communities that has not been invaded by F. japonica in the West Branch Susquehanna River valley (Pennsylvania, USA) as a baseline, this study examines whether and how this primarily intact riparian forest community differs from nearby invaded communities in terms of 1) native species richness, 2) native species density, and 3) riparian forest tree recruitment. Defining a baseline (intact) community composition will inform restoration plans for local riparian forests where knotweed might be eradicated or reduced. Invaded and non-invaded sites differed statistically across species richness, species density, and tree recruitment. Our results suggest that F. japonica has reduced the diversity and abundance of native understory riparian plant species. The species also appears to have suppressed long-term tree recruitment, setting up a trajectory whereby the eventual decline of trees currently in the canopy could shift this community from a tree-dominated riparian forest to a knotweed-dominated herbaceous shrubland.

New functionally dioecious bush tomato from northwestern Australia, Solanum ossicruentum, may utilize "trample burr" dispersal.

A new Australian species of functionally dioecious bush tomato of Solanum subgenus Leptostemonum is described. Solanum ossicruentum Martine & J.Cantley, sp. nov., is thought to be allied with members of the problematic "Dioicum Complex" lineage, but differs in its short silvery indumentum, long calyx lobes, larger stature, and an unusual fruit morphology that may represent "trample burr" seed dispersal. The species occurs in a range extending from the eastern Kimberley in Western Australia to far northwestern Northern Territory and has been recognized for decades as a variant of Solanum dioicum W.Fitzg. Specimens of this species were previously referred to by D.E. Symon and others as Solanum dioicum 'Tanami.' Ex situ crossing studies and SEM images of inaperturate pollen grains produced in morphologically hermaphrodite flowers indicate that this taxon is functionally dioecious. The scientific name was chosen with the help of 150 seventh grade life science students from Pennsylvania, USA.

Solanum watneyi, a new bush tomato species from the Northern Territory, Australia named for Mark Watney of the book and film "The Martian".

A new species of andromonoecious Solanum from the Australian "bush tomato clade" of Solanum subgenus Leptostemonum is described. Solanum watneyi Martine & Frawley, sp. nov. is closely allied with Solanum eburneum, and is sympatric with it in parts of its range in the Northern Territory. The new species has been recognized as a variant of Solanum eburneum for decades, at times being referred to by local botanists as Solanum sp. "Bullita" because of its relative abundance in the vicinity of the Bullita Station area of Judbarra/Gregory National Park. Morphometric analyses show that Solanum watneyi differs statistically from Solanum eburneum in several key reproductive and vegetative characters and field observations suggest that the two sister species may represent a case of edaphic speciation. We provide morphometric evidence for the novelty of Solanum watneyi, a complete description, and cite specimens for both species.

A new cryptically dioecious species of bush tomato (Solanum) from the Northern Territory, Australia.

A new species of dioecious Solanum from the Australian "Dioicum Complex" of Solanum subgenus Leptostemonum is described. Solanum cowiei Martine sp. nov., is allied with other members of this problematic lineage, but differs in its slender leaves, limited armature and diminutive habit. The species was first segregated by botanists at the Northern Territory Herbarium as Solanum sp. Litchfield (I.D. Cowie 1428); and specimens representing this species have also been referred to by Symon as Solanum sp. Fitzmaurice River. Collections suggest that this is an endemic of the sub-arid tropical zone of the Northern Territory. SEM images support initial assumptions that the new species is cryptically dioecious via production of inaperturate pollen grains in morphologically hermaphrodite flowers.