On the importance of sequence alignment inspections in plastid phylogenomics - an example from revisiting the relationships of the water-lilies

The water-lily clade represents the second earliest-diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, of which the "core Nymphaeaceae"-comprising the genera Euryale, Nymphaea and Victoria-is the most diverse clade. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. The length-variable introns and intergenic spacers are known to contain most of the sequence variability within the water-lily plastomes. Despite the challenges with multiple sequence alignment, any new molecular phylogenetic investigation on the core Nymphaeaceae should focus on these noncoding plastome regions. For example, a new plastid phylogenomic study on the core Nymphaeaceae should generate DNA sequence alignments of all plastid introns and intergenic spacers based on the principle of conserved sequence motifs. In this investigation, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomic analysis strategy in which all coding and noncoding partitions are separated and then undergo software-driven DNA sequence alignment, followed by a motif-based alignment inspection and adjustment. This approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through software algorithms alone. Our approach produces significantly different phylogenetic tree reconstructions for several of the plastome regions under study. The results of these reconstructions underscore that Nymphaea is paraphyletic in its current circumscription, that each of the five subgenera of Nymphaea is monophyletic, and that the subgenus Nymphaea is sister to all other subgenera of Nymphaea. Our results also clarify many evolutionary relationships within the Nymphaea subgenera Brachyceras, Hydrocallis and Nymphaea. In closing, we discuss whether the phylogenetic reconstructions obtained through our motif-based alignment adjustments are in line with morphological evidence on water-lily evolution.

Crop wild relatives of the United States require urgent conservation action

The contributions of crop wild relatives (CWR) to food security depend on their conservation and accessibility for use. The United States contains a diverse native flora of CWR, including those of important cereal, fruit, nut, oil, pulse, root and tuber, and vegetable crops, which may be threatened in their natural habitats and underrepresented in plant conservation repositories. To determine conservation priorities for these plants, we developed a national inventory, compiled occurrence information, modeled potential distributions, and conducted threat assessments and conservation gap analyses for 600 native taxa. We found that 7.1% of the taxa may be critically endangered in their natural habitats, 50% may be endangered, and 28% may be vulnerable. We categorized 58.8% of the taxa as of urgent priority for further action, 37% as high priority, and 4.2% as medium priority. Major ex situ conservation gaps were identified for 93.3% of the wild relatives (categorized as urgent or high priority), with 83 taxa absent from conservation repositories, while 93.1% of the plants were equivalently prioritized for further habitat protection. Various taxonomic richness hotspots across the US represent focal regions for further conservation action. Related needs include facilitating greater access to and characterization of these cultural-genetic-natural resources and raising public awareness of their existence, value, and plight.

Data for the calculation of an indicator of the comprehensiveness of conservation of useful wild plants

The datasets and code presented in this article are related to the research article entitled "Comprehensiveness of conservation of useful wild plants: an operational indicator for biodiversity and sustainable development targets"¹. The indicator methodology includes five main steps, each requiring and producing data, which are fully described and available here. These data include: species taxonomy, uses, and general geographic information (dataset 1); species occurrence data (dataset 2); global administrative areas data (dataset 3); eco-geographic predictors used in species distribution modeling (dataset 4); a world map raster file (dataset 5); species spatial distribution modeling outputs (dataset 6); ecoregion spatial data used in conservation analyses (dataset 7); protected area spatial data used in conservation analyses (dataset 8); and countries, sub-regions, and regions classifications data (dataset 9). These data are available at http://dx.doi.org/10.17632/2jxj4k32m2.1. In combination with the openly accessible methodology code (https://github.com/CIAT-DAPA/UsefulPlants-Indicator), these data facilitate indicator assessments and serve as a baseline against which future calculations of the indicator can be measured. The data can also contribute to other species distribution modeling, ecological research, and conservation analysis purposes.

Origins of food crops connect countries worldwide

Research into the origins of food plants has led to the recognition that specific geographical regions around the world have been of particular importance to the development of agricultural crops. Yet the relative contributions of these different regions in the context of current food systems have not been quantified. Here we determine the origins (‘primary regions of diversity’) of the crops comprising the food supplies and agricultural production of countries worldwide. We estimate the degree to which countries use crops from regions of diversity other than their own (‘foreign crops’), and quantify changes in this usage over the past 50 years. Countries are highly interconnected with regard to primary regions of diversity of the crops they cultivate and/or consume. Foreign crops are extensively used in food supplies (68.7% of national food supplies as a global mean are derived from foreign crops) and production systems (69.3% of crops grown are foreign). Foreign crop usage has increased significantly over the past 50 years, including in countries with high indigenous crop diversity. The results provide a novel perspective on the ongoing globalization of food systems worldwide, and bolster evidence for the importance of international collaboration on genetic resource conservation and exchange.

Application of the name Lemna punctata G. Mey., the type of Landoltia Les & D. J. Crawford

A recent (2011) attempt to change the previously designated type of the name of a duckweed species is discussed. Lemna punctata was first applied by Meyer in 1818 to a plant collected from South America, but original specimens have not been located. A prior neotype designation associated this name with a species native to parts of Asia, Australia and the Pacific, and widely introduced elsewhere, including South America. The species is generally treated by taxonomists in the genus Spirodela (either as S. punctata or the synonym S. oligorrhiza) or, more recently, as the sole member of the new (1999) genus Landoltia (as L. punctata). If accepted, this 2011 attempt to re-neotypify L. punctata would disrupt the names of two duckweed species as well as that of Landoltia. Nomenclatural arguments against accepting this new typification are provided, thereby supporting the continued usage of Landoltia in the sense intended by its original authors.

Poisonous plant vouchers

Every published report of plant poisoning, whether experimental or accidental, should document plant identification. The essential elements are: complete botanical Latin name including species, specific epithet and author(s); name of the collaborating botanist who identified the plant; and herbarium and collection number of a voucher specimen from the exposure lot. Additional information to aid identification might include plant photographs, drawings, and descriptions.

Retrospective searching for poisonous plant vouchers

Few published reports of plant poisoning, whether experimental or accidental, document vouchers. This can be rectified by retrospective location of vouchers through determination of a collaborating botanist or herbarium of deposit. An absolute voucher is referenced in the toxicology report. For a probable voucher the report does not identify an herbarium specimen, but the report and the specimen label or sheet agree on plant name, collector's name, collection date and place. A possible voucher is perhaps from the exposure lot, but was collected by the collaborating botanist at a somewhat earlier or later date than the exposure date. On the other hand, a supporting specimen was collected by the collaborating botanist but is not from the exposure lot. Vouchers and supporting specimens for some species of Asclepias tested for toxicity by CD Marsh and coworkers were found in the US National Herbarium at the Smithsonian Institution, Washington DC.