•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 res...

The Solanaceae are among the most diverse families in the Peruvian flora, with about 42 genera and 600 species (Brako & Zarucchi, 1993; Ulloa Ulloa et al., 2004), mostly herbs and shrubs. Here we recognize as endemics 203 species and six varieties in 16 genera. This family ranks 6th among the most diverse families in endemic taxa. Solanum, Nolana and Jaltomata are the genera with more endemic species. Endemic taxa are found in almost all regions, mainly Mesoandean, Very Humid Montane Forests and Subtropical Costal Desert, from sea level 100 to 3800 m elevation. Thirty-six taxa have been recorded within Peru’s protected areas system.

La familia Solanaceae es una de las más ricas en especies en la flora peruana, siendo reconocida con alrededor de 42 géneros y 600 especies (Brako & Zarucchi, 1993; Ulloa Ulloa et al., 2004), principalmente hierbas y arbustos. En este trabajo reconocemos 208 especies y seis variedades como endémicos, en 16 géneros. Esta familia ocupa el sexto lugar por su diversidad en especies endémicas, siendo Solanum, Nolana y Jaltomata los géneros más ricos en especies. Los taxones endémicos se encuentran en la mayoría de las regiones, principalmente en Mesoandina, Desierto Semicálido Tropical y Bosques Muy Húmedos Montanos, desde el nivel del mar hasta los 3800 m de altitud. Treinta y seis taxones se encuentran representados dentro del Sistema Nacional de Áreas Naturales Protegidas por el Estado.

Plant scientists make inferences and predictions from phylogenetic trees to solve scientific problems. Crop losses due to disease damage is an important problem that many plant breeders would like to solve, so the ability to predict traits like disease resistance from phylogenetic trees derived from diverse germplasm would be a significant approach to facilitate cultivar improvement. Alternaria leaf blight (ALB) is among the most devastating diseases of carrots (Daucus spp., Apiaceae) worldwide. Thus, new approaches to identify resistant germplasm to this disease are needed. In a study of 106 accessions of wild and cultivated Daucus and related genera, we determined plant height is the best explanatory variable to predict ALB resistance using a phylogenetic linear regression model. Using the estimated area under the disease progress curve, the most resistant species to ALB were the non-c...

•Premise of study: Molecular phylogenetics of genome‐scale data sets (phylogenomics) often produces phylogenetic trees with unprecedented resolution. A companion phylogenomics analysis of Daucus using 94 conserved nuclear orthologs supported many of the traditional species but showed unexpected results that require morphological analyses to help interpret them in a practical taxonomic context. •Methods: We evaluated character state distributions, stepwise discriminant analyses, canonical variate analyses, and hierarchical cluster analyses from 40 morphological characters from 81 accessions of 14 taxa of Daucus and eight species in related genera in an experimental plot. •Key results: Most characters showed tremendous variation with character state overlap across many taxa. Multivariate analyses separated the outgroup taxa easily from the Daucus ingroup. Concordant with molecular ...

•Premise of the study: We explored the utility of multiple nuclear orthologs for the taxonomic resolution of wild and cultivated carrot, Daucus species. •Methods: We studied the phylogeny of 92 accessions of 13 species and two subspecies of Daucus and 15 accessions of related genera (107 accessions total) with DNA sequences of 94 nuclear orthologs. Reiterative analyses examined data of both alleles using ambiguity codes or a single allele with the highest coverage, trimmed vs. untrimmed homopolymers; pure exonic vs. pure intronic data; the use of all 94 markers vs. a reduced subset of markers; and analysis of a concatenated data set vs. a coalescent (species tree) approach. •Key results: Our maximum parsimony and maximum likelihood trees were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades. They resolved multiple accessions of m...

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 Pe...

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 ...

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 morphol...

Daucus has traditionally been estimated to comprise 21–25 species, but a recent study expanded the genus to c. 40 species. The present study uses ten nuclear orthologues to examine 125 accessions, including 40 collections of 11 species (D. annuus, D. arcanus, D. decipiens, D. durieua, D. edulis, D. gracilis, D. minusculus, D. montanus, D. pumilus, D. setifolius and D. tenuissimus) newly examined with nuclear orthologues. As in previous nuclear orthologue studies, Daucus resolves into two well-defined clades, and groups different accessions of species together. Maximum likelihood and maximum parsimony analyses provide concordant results, but SVD quartets reveals many areas of disagreement of species within these two major clades. With maximum likelihood and maximum parsimony analyses Daucus montanus (hexaploid) is resolved as an allopolyploid between D. pusillus (diploid) and D. glochid...

The genus Solanum is among the most species-rich genera both of the Peruvian flora and of the tropical Andes in general. The present revised checklist treats 276 species of Solanum L., of which 253 are native, while 23 are introduced and/or cultivated. A total of 74 Solanum species (29% of native species) are endemic to Peru. Additional 58 species occur only in small number of populations outside Peru, and these species are here labelled as near-endemics to highlight the role Peru playes in their future protection. Species diversity is observed to peak between 2500 – 3000 m elevation, but endemic species diversity is highest between 3000 – 3500 m elevation. Cajamarca has the highest number of endemic (29 spp.) and total species (130 spp.), even when considering the effect of area. Centers of endemic species diversity are observed in provinces of Cajamarca (Cajamarca), Huaraz and Carh...

The genus Solanum is among the most species-rich genera both of the Peruvian flora and of the tropical Andes in general. The present revised checklist treats 276 species of Solanum L., of which 253 are native, while 23 are introduced and/or cultivated. A total of 74 Solanum species (29% of native species) are endemic to Peru. Additional 58 species occur only in small number of populations outside Peru, and these species are here labelled as near-endemics to highlight the role Peru playes in their future protection. Species diversity is observed to peak between 2500 – 3000 m elevation, but endemic species diversity is highest between 3000 – 3500 m elevation. Cajamarca has the highest number of endemic (29 spp.) and total species (130 spp.), even when considering the effect of area. Centers of endemic species diversity are observed in provinces of Cajamarca (Cajamarca), Huaraz and Carh...