Integrated Molecular and Morphological Studies of the Daucus guttatus Complex (Apiaceae)

In a previous study using 94 nuclear orthologs, we reported the species status of the Daucus guttatus complex to be unresolved, partitioned into three clades. In the present study, a subset of ten of these 94 orthologs was used to infer the phylogeny of the D. guttatus complex and related species. A near parallel set of accessions, planted in a common garden, was used for morphological analyses. The molecular trees are highly resolved for most of the clades, grouping accessions of the D. guttatus complex into four clades. Bayesian concordance analysis and a coalescent approach gave slightly different topologies. Morphological data likewise support four taxa in the complex. Moreover, herbarium research from a companion study informs nomenclature for taxa of the complex. We identify these four clades as D. bicolor, D. conchitae, D. guttatus, and D. setulosus; internested in or among these segregates are the phenetically distinctive species D. glochidiatus, D. involucratus, D. littoralis, and D. pusillus. Our research redefines species variation in the D. guttatus complex, clarifies species names, interspecific relationships, confirms a useful subset of nuclear orthologs for studies of dominant topologies of Daucus, and discovers morphological characters allowing proper identification of the four species of the D. guttatus complex and related species

Lectotype Designation for Seven Species Names in the Daucus guttatus Complex (Apiaceae) from the Central and Eastern Mediterranean Basin

The Daucus guttatus complex includes two to four species growing from central and northern Italy to the Middle East. They are characterized by being typically annuals up to 50 cm high; with primary umbels up to 7 cm in diameter with fewer than 25(35) rays; discolored umbels frequent, bearing one to several dark colored umbellules which form different color patterns; and mericarps relatively small, ca. 2.0‐4.5 mm. The taxonomy of this complicated group has not been satisfactorily resolved to date and is the focus of current research. Seven names of species belonging to the D. guttatus complex occurring in the central and eastern Mediterranean basin are typified here: Daucus guttatus, Daucus bicolor, Daucus involucratus, Daucus setulosus, Daucus broteri, Daucus hirsutus, and Daucus speciosus. Historical data are reported to justify lectotype and/or epitype selection, and selected morphological and distributional data are used to facilitate identification. The resulting typifications will enable proper naming of clades identified in the accompanying integrated molecular and morphological study, clarifying the taxonomy of the Daucus guttatus complex

New MRI, 18F-DOPA and 11C-(+)-alpha-dihydrotetrabenazine templates for Macaca fascicularis neuroimaging: advantages to improve PET quantification

Normalization of neuroimaging studies to a stereotaxic space allows the utilization of standard volumes of interest (VOIs) and voxel-based analysis (SPM). Such spatial normalization of PET and MRI studies requires a high quality template image. The aim of this study was to create new MRI and PET templates of 18F-DOPA and 11C-(+)-α-dihydrotetrabenazine (11C-DTBZ) of the Macaca fascicularis brain, an important animal model of Parkinson's disease. MRI template was constructed as a smoothed average of the scans of 15 healthy animals, previously transformed into the space of one representative MRI. In order to create the PET templates, 18F-DOPA and 11C-DTBZ PET of the same subjects were acquired in a dedicated small animal PET scanner and transformed to the created MRI template space. To validate these templates for PET quantification, parametric values obtained with a standard VOI-map applied after spatial normalization to each template were statistically compared to results computed using individual VOIs drawn for each animal. The high correlation between both procedures validated the utilization of all the templates, improving the reproducibility of PET analysis. To prove the utility of the templates for voxel-based quantification, dopamine striatal depletion in a representative monkey treated with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) was assessed by SPM analysis of 11C-DTBZ PET. A symmetric reduction in striatal 11C-DTBZ uptake was detected in accordance with the induced lesion. In conclusion, templates of M. fascicularis brain have been constructed and validated for reproducible and automated PET quantification. All templates are electronically available via the internet

Genetic Diversity and Population Structure Assessed by SSR in a Peruvian Germplasm Collection of Loche Squash (Cucurbita moschata, Cucurbitaceae)

Loche is an ancient landrace of squash from Northern Peru, notable for its vegetative reproduction and lack of seeds in fruits. To date, very little is known about its genetics. Here, we used 21 simple sequence repeats to assess the genetic diversity and population structure of a collection of 100 samples of loche from three localities in Peru, and 10 samples of related species, C. pepo and C. maxima (110 accessions in total). A total 85 bands were manually scored, obtaining an average of 4.05 alleles per locus. The UPGMA clustering method and principal coordinate analysis showed a clear identification between the three species of Cucurbita. Population structure analysis clustered the 110 accessions into the following five populations: (i) three of loche, (ii) one of C. pepo, and (iii) one of C. maxima. Genetic diversity estimation was conducted considering only the three groups (populations) of loche identified, which was 0.024 as an average. AMOVA revealed the greatest variation between populations (79.66%) and indicated that variability within populations is 20.33%. Vegetative propagation by means of stem cuttings and cultivation in a very restricted geographical area would explain the rather low diversity of loche. This in turn would suggest that the apparent variation observed in fruit shape may be explained by somatic mutation and/or environmental factors

Greatly reduced phylogenetic structure in the cultivated potato clade (Solanum section Petota pro parte)

•Premise of the Study: osible ies boundaries of wild and cultivated potatoes are controversial, with osible the taxonomic problems in the cultivated potato clade. We here provide the first in‐depth phylogenetic study of the cultivated potato clade to explore osible causes of these problems. •Methods: We examined 131 diploid accessions, using 12 nuclear orthologs, producing an aligned data set of 14,072 DNA characters, 2171 of which are parsimony‐informative. We analyzed the data to produce phylogenies and perform concordance analysis and goodness‐of‐fit tests. •Key Results: There is good phylogenetic structure in clades traditionally referred to as clade 1+2 (North and Central American diploid potatoes exclusive of Solanum verrucosum), clade 3, and a newly discovered basal clade, but drastically reduced phylogenetic structure in clade 4, the cultivated potato clade. The results highlight a clade of species in South America not shown before, ‘neocardenasii’, sister to clade 1+2, that possesses key morphological traits typical of diploids in Mexico and Central America. Goodness‐of‐fit tests suggest potential hybridization between some species of the cultivated potato clade. However, we do not have enough phylogenetic signal with the data at hand to explicitly estimate such hybridization events with species networks methods. •Conclusions: We document the close relationships of many of the species in the cultivated potato clade, provide insight into the cause of their taxonomic problems, and support the recent reduction of species in this clade. The discovery of the neocardenasii clade forces a reevaluation of a hypothesis that section Petota originated in Mexico and Central America

Influence of arboreal components on the physical-chemical characteristics of the soil under four silvopastoral systems in northeastern Peru

Silvopastoral systems (SPS) are presented as an alternative for the protection and recovery of soils; however, the relationship between the tree component and the physical-chemical characteristics of the soil is unknown. Thus, the objective of this study was to evaluate the physical-chemical characteristics of the soil under four silvopastoral systems (SPS), alder (Alnus acuminata), pine (Pinus patula), cypress (Cupressus macrocarpa), and pona (Ceroxylon quindiuense), and a treeless system (TS) in the Amazonas region. A completely randomized design (CRD) with five treatments and three replicates was used. The experimental units were sampled at two depths, 0–15 and 15–30 cm. The parameters evaluated were pH, electrical conductivity (dS/m), organic matter (%), phosphorus (ppm), potassium (ppm), cation exchange capacity (meq/100 g), porosity (%), mechanical resistance (kg/cm2), bulk density (gr/cm3), moisture (%) and total carbon (t/ha). The results were analyzed by analysis of variance (α = 0.05 %) and Tukey's test of means (p ≤ 0.05). The systems presented strong acidic pH values (4.11–5.61), which resulted in high organic matter contents in all systems (6.74–9.99 %). The highest phosphorus content was in the SPS with alder (12.64 ppm), and the highest potassium content was in the SPS with cypress (382.33 ppm). Porosity in all systems was higher than 60 %. The highest bulk density was between 15 and 30 cm, and the highest percentage of moisture was in the surface layer (0–15 cm). The mechanical strength was higher in the SPS with cypress (2.62 kg/cm2). For all the systems evaluated, the highest carbon stock was found in the first 15 cm. The SPS with pine had the best soil characteristics and carbon sequestration (149.05 t/ha)

Employing a Nondestructive Method for the Estimation of Foliar Area of Quina (Cinchona officinalis)

Leaf area is related to tree growth, water balance, and mechanical resistance to physical and biotic agents. Given its importance, the purpose of the study was to compare two nondestructive methods of leaf area estimation using the free software ImageJ vs. graph paper in seedlings of quina tree. Three young and mature leaves were evaluated on 18 quina seedlings. Descriptive statistics were obtained, and both methods were compared using the Kruskal–Wallis test, and a regression equation was estimated based on leaf width and length

Additional file 1 Table S1

Additional file 1: Table S1. The 162 accessions of Daucus, and two accessions of related genera characterized in this study, improvement status, locality information and new identification

Additional file 12 Figure S10

Additional file 12: Figure S10. Box plot analyses of the 23 morphological characters examined for members of Daucus carota complex (subsp. sativus not included) in this study. The box plot displays individual plant values for median, 25% and 75% percentile, range, and outliers

Data from: Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

Background: The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the D. carota complex. Results: We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30 % missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10 % with a total of 18,565 SNPs, and (ii) rate of missing data 30 %, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic. Conclusions: Our study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus