The use and limits of AFLP data in the taxonomy of polyploid wild potato species in Solanum series Conicibaccata

Solanum sect. Petota (tuber-bearing wild and cultivated potatoes) are a group of approximately 190 wild species distributed throughout the Americas from the southwestern United States south to Argentina, Chile, and Uruguay. Solanum series Conicibaccata are a group of approximately 40 species within sect. Petota, distributed from central Mexico to central Bolivia, composed of diploids (2n = 2x = 24), tetraploids (2n = 4x = 48) and hexaploids (2n = 6x = 64); the polyploids are thought to be polysomic polyploids. This study initially was designed to address species boundaries of the four Mexican and Central American species of series Conicibaccata with AFLP data with the addition of first germplasm collections of one of these four species, Solanum woodsonii, as a follow-up to prior morphological, chloroplast DNA, and RAPD studies; and additional species of series Conicibaccata from South America. AFLP data from 12 primer combinations (1722 polymorphic bands) are unable to distinguish polyploid species long thought to be distinct. The data suggest a complex reticulate history of the tetraploids or the need for a broad downward reevaluation of the number of species in series Conicibaccata, a trend seen in other series of sect. Petota. Separately, through flow cytometry, we report the first ploidy level of S. woodsonii, as tetraploid (2n = 48). The U.S. Government’s right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

Allelism of Endosperm Balance Number (EBN) in Mexican tuber-bearing Solanum species

Summary Endosperm Balance Number (EBN) is a genetic, dose-dependent crossability system functioning in tuber-bearing Solanum species. Each species has been assigned 1EBN, 2EBN, or 4EBN. Species thus designated cross only within their EBN group. Doubling of chromosome number also doubles the EBN. The ploidy: EBN ratio is not consistent among Solanum species. Some diploids are 2EBN while others are 1EBN. Some tetraploids are 4EBN while others are 2EBN. Species from Mexico typically have EBNs that are one-half of their ploidy [e.g. 2x(1EBN), 4x(2EBN)]. Hybrids of Mexican species and a South American species, 2x(1EBN) S. Commersonii, and its 4x(2EBN) colchicine derivative were made and crossed to 1, 2, and 4EBN standard testers to determine the relationship of the genetic organization of EBN among and within these species. Diploid hybrids crossed only to 1EBN standard testers. Hybrids of 4x(2EBN) S. commersonii and 4x(2EBN) Mexican species crossed almost exclusively to 2EBN standard testers. Complex tetraploid hybrids involving S. commersonii, S. stenophyllidium (a Mexican diploid), and Mexican tetraploids of series Longipedicellata also crossed only to 2EBN testers. The apparent lack of recombination and segregation for EBN in these hybrids indicates that the genomes of the Mexican diploid and tetraploid species carry EBN in a way genetically similar to that of the South American species S. Commersonii.Cooperative investigation of the U.S. Department of Agriculture, Agricultural Research Service and the Wisconsin Experiment Station. Supported in part by the USDA/Cooperative States Research Service Competitive Grant No. 83-CRCR-1-1253     

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

Premise of the Study

The species boundaries of wild and cultivated potatoes are controversial, with most of the taxonomic problems in the cultivated potato clade. We here provide the first in‐depth phylogenetic study of the cultivated potato clade to explore possible 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.     

Mitochondrial DNA Variation and Phylogeography of the Ferruginous Pygmy-Owl (Glaucidium brasilianum)

Sequences from the mitochondrial cytochrome b gene were used to examine patterns of variation within and among populations of the ferruginous pygmy-owl (Glaucidium brasilianum) from both North America (including populations from Mexico) and South America. As currently conceived, G. brasilianum is paraphyletic, with North American and South American clades representing two distinct groups that should be recognized as the distinct species G. ridgwayi and G. brasilianum, respectively. Within the G. ridgwayi clade, populations from Arizona, Sonora, and Sinaloa are genetically distinct and share no mitochondrial haplotypes with populations occurring in Texas and other regions of Mexico. According to nested clade analysis this separation may be the consequence of past fragmentation that predates the origin of the Sonora desert. In addition, gene flow between the Arizona/Sonora/Sinaloa populations and the Texas/other Mexico populations is practically nonexistent, with estimates being approximately one individual every 10 generations. Collectively, these data suggest that the Arizona/Sonora/Sinaloa clade should be recognized as either a distinct subspecies or phylospecies from the group containing populations in Texas and the remainder of Mexico. These data should be used as guidelines for pygmy-owl recovery and conservation, as they meet the recommendations of task 3 of the pygmy-owl recovery plan that lists genetic data as essential information for pygmy-owl management.     

Genetic variation in photosynthetic characteristics among invasive and native populations of reed canarygrass (Phalaris arundinacea)

With the extensive spread of invasive species throughout North America and Europe there is an urgent need to better understand the morphological and physiological characteristics of successful invasive plants and the evolutionary mechanisms that allow introduced species to become invasive. Most ecological studies have focused on morphological differences and changes in community dynamics, and physiological studies have typically explored the differences between native and invasive species. In this study, 15 different genotypes of Phalaris arundinacea from both its native (European) and invasive (North American) range were grown in a common garden experiment to monitor the physiological differences between native and invasive genotypes. Here we present data that suggests high variability exists in the physiological traits among genotypes of P. arundinacea, yet genotypes from the native range are not necessarily physiologically inferior to the hybridized invasive genotypes. Previous work has shown that multiple introductions of P. arundinacea from various European locations to the United States resulted in numerous hybridization events, yielding more genetic variability and phenotypic plasticity in the invasive range. Of the genotypes studied, both morphological and physiological traits of genotypes with French origin were significantly different from the plants from the Czech Republic, North Carolina, and Vermont. The lack of clear differences between native and invasive genotypes indicates that physiological traits may be highly conserved in P. arundinacea and enhanced photosynthetic rates are not indicative of successful invasive genotypes. Instead, morphological traits and defensive secondary compound metabolism may play a more important role in the success of P. arundinacea within its invasive range, and patterns of genetic variation in physiological traits between invasive and native range may be more important than the mean traits of each region when explaining reed canarygrass’ invasive potential in North America.     

Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data

Species in the genus Castanea are widely distributed in the deciduous forests of the Northern Hemisphere from Asia to Europe and North America. They show floristic similarity but differences in chestnut blight resistance especially among eastern Asian and eastern North American species. Phylogenetic analyses were conducted in this study using sequences of three chloroplast noncoding trnT-L-F regions. The trnT-L region was found to be the most variable and informative region. The highest proportion of parsimony informative sites, more and larger indels, and higher pairwise distances between taxa were obtained at trnT-L than at the other two regions. The high A+T values (74.5%) in the Castanea trnT-L region may explain the high proportion of transversions found in this region where as comparatively lower A+T values were found in the trnL intron (68.35%) and trnL-F spacer (70.07%) with relatively balanced numbers of transitions and transversions. The genus Castanea is supported as a monophyletic clade, while the section Eucastanon is paraphyletic. C. crenata is the most basal clade and sister to the remainder of the genus. The three Chinese species of Castanea are supported as a single monophyletic clade, whose sister group contains the North American and European species. There is consistent but weak support for a sister–group relationship between the North American species and European species.     

Phylogenetic relationships and biogeographic patterns in North American members of Carex section Acrocystis (Cyperaceae) using nrDNA ITS and ETS sequence data

Carex section Acrocystis currently includes 27 taxa in North America. Recent phylogenetic studies have suggested that the North American and some but not all of the Eurasian species form a clade. Relationships and biogeographic patterns among species in this core-Acrocystis group are explored here using nuclear ribosomal (nrDNA) internal transcribed spacer region (ITS) and nrDNA external transcribed spacer region (ETS) sequence data. While maximum parsimony analysis of the ITS and ETS data provides only a moderately resolved branching structure for species relationships within the core-Acrocystis clade, maximum likelihood analysis provides a more resolved hypothesis of relationships in the section. The core-Acrocystis clade consists of a grade of Eurasian and primarily western North American species, with a well-supported clade of only eastern North American species nested within this grade. ITS and ETS types do not coalesce within many species or species complexes. Possible explanations for the non-coalescent nature of ITS and ETS copies in Acrocystis are explored, including lineage sorting, hybridization, and cryptic species.     

Nuclear DNA markers of the Australian tetraploid Microseris scapigera and its North American diploid relatives

The allotetraploid lactucean Microseris scapigera of Australia and New Zealand has presumably arisen in western North America by hybridization between an annual and a perennial diploid species followed by polyploidization and long-distance dispersal. A phylogenetic tree of various North American diploids, based on RFLPs in the nuclear DNA, confirmed the division of the genus into a clade containing the diploid annuals and a clade containing the diploid perennials. Four RFLP markers were shared among all accessions of M. scapigera and all the diploid accessions. Twelve markers found in the outgroup (Uropappus lindleyi) were absent in all Microseris. A cladogram of plants from six populations of M. scapigera based on eight RFLP markers shows a progressive specialization of three clades of two populations each. Two populations without any markers differentiating them from the North American diploids form the basic clade. These consist of plants with an apparently derived morphology that are self-compatible (or agamospermic) and thereby differ from most M. scapigera. Few markers in M. scapigera could be attributed to one or the other parental genome. As yet, we have found only one ITS 1 sequence of the nuclear ribosomal cistrons in M. scapigera. This sequence has features of both parental sequences.     

Monophyly and phylogenetic relationships of Minthostachys (Labiatae, Nepetoideae) examined using morphological and nrITS data

Minthostachys (Benth.) Spach (Labiatae) from Andean South America was long held to be closely related to Macaronesian Bystropogon L’Hér. or to North American Pycnanthemum Michx. The possibility of a close relationship to elements of South American Satureja/Clinopodium s.l. is here proposed for the first time, and a phylogenetic analysis of nrITS data is employed to test the competing hypotheses. For Minthostachys and its putative closest relatives, the possible evolution of morphological characters is investigated with a cladistic analysis. The results suggest that Minthostachys is nested in a clade of South American Mentheae, and probably in the former genus Xenopoma Willd., a group of small-flowered, bee-pollinated species currently included in Clinopodium L.. Minthostachys is considered monophyletic based on nrITS data and its scandent habit.     

Mitochondrial DNA and RAPD polymorphisms in the haploid mite Brevipalpus phoenicis (Acari: Tenuipalpidae)

Brevipalpus phoenicis (Geijskes) (Acari: Tenuipalpidae) is recognized as the vector of citrus leprosis virus that is a significant problem in several South American countries. Citrus leprosis has been reported from Florida in the past but no longer occurs on citrus in North America. The disease was recently reported in Central America, suggesting that B. phoenicis constitutes a potential threat to the citrus industries of North America and the Caribbean. Besides B. phoenicis, B. obovatus Donnadieu, and B. californicus (Banks) have been incriminated as vectors of citrus leprosis virus and each species has hundreds of host plants. In this study, Brevipalpus mite specimens were collected from different plants, especially citrus, in the States of Florida (USA) and São Paulo (Brazil), and reared on citrus fruit under standard laboratory conditions. Mites were taken from these colonies for DNA extraction and for morphological species identification. One hundred and two Random Amplified Polymorphic DNA (RAPD) markers were scored along with amplification and sequencing of a mitochondrial cytochrome oxidase subunit I gene fragment (374 bp). Variability among the colonies was detected with consistent congruence between both molecular data sets. The mites from the Florida and Brazilian colonies were morphologically identified as belonging to B. phoenicis, and comprise a monophyletic group. These colonies could be further diagnosed and subdivided geographically by mitochondrial DNA analysis.     

Molecular phylogeny of the Acre clade (Crassulaceae): Dealing with the lack of definitions for Echeveria and Sedum

The phylogenetic relationships within many clades of the Crassulaceae are still uncertain, therefore in this study attention was focused on the “Acre clade”, a group comprised of approximately 526 species in eight genera that include many Asian and Mediterranean species of Sedum and the majority of the American genera (Echeveria, Graptopetalum, Lenophyllum, Pachyphytum, Villadia, and Thompsonella). Parsimony and Bayesian analyses were conducted with 133 species based on nuclear (ETS, ITS) and chloroplast DNA regions (rpS16, matK). Our analyses retrieved four major clades within the Acre clade. Two of these were in a grade and corresponded to Asian species of Sedum, the rest corresponded to a European–Macaronesian group and to an American group. The American group included all taxa that were formerly placed in the Echeverioideae and the majority of the American Sedoideae. Our analyses support the monophyly of three genera – Lenophyllum, Thompsonella, and Pachyphytum; however, the relationships among Echeveria, Sedum and the various segregates of Sedum are largely unresolved. Our analyses represents the first broad phylogenetic framework for Acre clade, but further studies are necessary on the groups poorly represented here, such as the European and Asian species of Sedum and the Central and South American species of Echeveria.     

Host specificity ofPterolonche inspersa [Lep.: Pterolonchidae] and its potential as a biological control agent forCentaurea diffusa,diffuse knapweed,andC. Maculosa,spotted knapweed

In 1981 the United States Department of Agriculture (USDA) Biological Control of Weeds Laboratory (BCWL, Rome, Italy) started investigating the host specificity ofP. inspersa as a candidate for biological control ofC. diffusa andC. maculosa, and in 1985 the investigation was completed at the USDA Biological Control of Weeds Laboratory at Albany, California. Thirty five species of plants in the familyAsteraceae and 23 other species in 8 related families were tested. Larval survival beyond 1st instar occurred only onCentaurea spp. except for 1 larva found inCnicus benedictus L.P. inspersa is stenophagous onCentaurea, therefore, a good candidate for introduction into North America.      

Seven new calochroid and fulvoid species of Cortinarius

We describe seven new European species of Cortinarius. All species are based on analyses of morphological and DNA sequence data. They all belong to a well-supported clade comprising most species traditionally treated in Cortinarius subgenus Phlegmacium sections Fulvi and Calochroi (i.e. the/Calochroi clade). All taxa are either fulvoid (containing anthraquinoid pigments) or calochroid (without these pigments). Morphological and ecological data are presented for all species and compared with similar species. A dichotomous key is presented for C. calochrous and similar species, including all six newly described calochroid species. The calochroid species C. albertii, C. chailluzii, C. cisticola, C. sancti-felicis, C. selandicus and C. vesterholtii spp. nov., and the fulvoid species C. langeorum sp. nov. are described.     

AFLP markers support separation of Solanum nodiflorum from Solanum americanum sensu stricto (Solanaceae)

This study was aimed at examining the relationships between the African material of Solanum americanum (also designated as S. nodiflorum), accessions of this taxon from other geographical areas, and American S. americanum using AFLP markers. 96 individuals representing 39 accessions of S. americanum sensu lato and related diploid species from the widest possible geographical range, and one accession of S. dulcamara (as outgroup) were used. The AFLP results suggested that American S. americanum differs from S. nodiflorum and that the material investigated in this study can be assigned to three different species: S. americanum sensu stricto, S. nodiflorum and a Solanum species from Brazil. These species can be differentiated based on a combination of floral and fruit characteristics.     

Genetic biogeography of the rate “copper moss”,Scopelophila cataractae (Pottiaceae)

Scopelophila cataractae, one of the so-called copper mosses, has a broad geographic distribution that includes North, Central, and South America, Europe, and Asia, but is rare throughout its range. A genetic analysis of 32 populations from the United States, Europe, and Asia based on 15 putative allozyme loci indicates that levels of genetic diversity vary among geographic regions. Six European populations are fixed for the same alleles at all 15 loci, consistent with the hypothesis thatS. cataractae is a recent immigrant in that region. The species is more diverse in the U.S., where it appears to be native. Five populations collected on copper-enriched soils around shrines and temples in Tokyo are genetically monomorphic, but Asian populations from another Japanese site, India, and Nepal are exceptionally diverse in terms of numbers of alleles and multilocus haplotypes, total gene diversity (H_T), and in the degree of differentiation among populations (measured as Nei'sI andD). Long-distance dispersal has probably played an important role in the geographic history ofS. cataractae, but the species appears to be native in both the New and Old Worlds. Gene flow between plants disjunct on different continents is insufficient to explain the lack of geographically correlated morphological and genetic differentiation inS. cataractae.     

Marbleseeds are gromwells – Systematics and evolution of Lithospermum and allies (Boraginaceae tribe Lithospermeae) based on molecular and morphological data

Phylogenetic relationships are complex within the Lithospermeae, a large subgroup of the Boraginaceae s.str. The relationships of New World Lasiarrhenum, Macromeria, Nomosa, Onosmodium, Perittostoma, and Psilolaemus to subcosmopolitan and much larger Lithospermum have not been critically investigated in the recent past. No molecular data on the phylogeny of these genera and Lithospermum have so far been published. We investigated the relationships within Lithospermeae using three loci (nuclear ITS plus 5.8S rRNA, chloroplast trnL-F-spacer, and trnS-G-spacer) and micromorphological character traits (pollen, nutlets). Lithospermum s.l. constitutes the sistergroup of Asian Ulugbekia and is monophyletic only when its American segregates “Macromeria”, monotypic Nomosa, and Onosmodium are included. Both the African and the South American species groups of Lithospermum are monophyletic, but North American representatives are not resolved in a single clade. Morphological characters that have been considered as important for generic delimitation in the past (such as large, yellow corollas without faucal scales, particular pollen types, coarsely veined leaves, shrubby habit) have evolved in at least two only distantly related lineages within Lithospermum s.l. The reduction of American “Macromeria”, Nomosa, and Onosmodium as well as Asian Ulugbekia under Lithospermum is proposed to render the latter monophyletic. This redefined Lithospermum s.l. appears to have undergone a type of recent “island radiation” in the Americas, reflected in a morphological diversity far exceeding that found in the Old World.     

Molecular phylogeny of Cypripedium (Orchidaceae: Cypripedioideae) inferred from multiple nuclear and chloroplast regions

A molecular analysis was performed on 56 taxa in the orchid genus Cypripedium using nrDNA ITS and five chloroplast regions (trnH-psbA, atpI-atpH, trnS-trnfM, trnL-F spacer, and the trnL intron). The genus Cypripedium was confirmed as monophyletic. Our data provided strong support for monophyletic grouping of eight infrageneric sections (Subtropica, Obtusipetala, Trigonopedia, Sinopedilum, Bifolia, Flabelinervia, Arietinum, and Cypripedium) defined in earlier taxonomic treatments, and paraphyletic grouping of two sections (Irapeana and Retinervi). Within the genus Cypripedium, the first divergent lineage consisted of two Mesomaerican species, and subsequently the Cypripedium debile lineage from eastern Asia was split. Our study did not support the notion that two Asian species (Cypripedium subtropicum and Cypripedium singchii) were closely related to either Mesoamerican Cypripedium irapeanum or North American Cypripedium californicum, as indicated by previous interpretations based on morphological evidences. In addition, one pair of vicariant species, Cypripedium plectrochilum (eastern Asia) and Cypripedium arietinum (North America), unique to section Arietinum, was confirmed. Furthermore, within the monophyletic section Cypripedium two previously recognized subsections, Cypripedium and Macrantha, were shown to be paraphyletic. Our results suggested that this section split into two groups based on distribution (North America vs. Eurasia) instead of such previously used, morphological traits as flower color, and the shape of the lips (labellum) and lateral petals.     

Reconciling classical and molecular phylogenies in the stichotrichines (Ciliophora, Spirotrichea), including new sequences from some rare species

We performed a comparative morphological and molecular study on oxytrichid and urostylid stichotrichs (=part of the former hypotrichs). Included are new small subunit (18S) ribosomal RNA (rRNA) gene sequences from five rare oxytrichids (Gonostomum namibiense, Cyrtohymena citrina, Hemiurosoma terricola, Onychodromopsis flexilis, Orthoamphisiella breviseries) and published sequences, based on cultures provided by the senior author, of two key stichotrichid genera, viz., Gastrostyla and Engelmanniella. These and other sequences, altogether 27 species representing 23 genera, were used to analyze how 18S rRNA-based phylogenetic trees can be reconciled with the morphological and ontogenetical data. In 18S rRNA trees, the oligotrichine family Halteriidae invariably clusters within the oxytrichid clade, usually near Oxytricha granulifera, type species of the genus. This position is hardly supported by morphological and ecological evidence and, especially, it contradicts the current ontogenetic findings; possibly, it is an artifact caused by taxa undersampling and/or special molecular evolutionary events. In contrast, most morphological and DNA sequence data of the stichotrichs can be harmonized with the CEUU (Convergent Evolution of Urostylids and Uroleptids) hypothesis which suggests that the urostylid midventral pattern evolved from an oxytrichine ancestor, developing a second time within the Oxytrichidae. The systematic position of one of the two key genera could be clarified with the 18S rRNA sequences: Gastrostyla is a stylonychine oxytrichid. Based on the molecular data and a reassessment of ontogenesis, a new genus, Styxophrya nov. gen., is established for Onychodromus quadricornutus Foissner, Schlegel & Prescott, 1987.     

Two new species of yellow-shouldered bats,genus Sturnira Gray, 1842 (Chiroptera,Phyllostomidae) from Costa Rica,Panama and western Ecuador

Two new species of yellow-shouldered bats Sturnira Gray, 1842 (Chiroptera, Phyllostomidae) from Central America and western South America are described using molecular and morphological data. The two new species, which occur in Costa Rica and Panama and in western Ecuador, were previously confused with S. ludovici, and S. lilium and S. luisi, respectively. Sturnira now includes 22 described species, making it the most speciose genus in the Neotropical family Phyllostomidae.     

Phylogenetic analysis of Fosterella L.B. Sm. (Pitcairnioideae, Bromeliaceae) based on four chloroplast DNA regions

The about 31 species of Fosterella L.B. Sm. (Bromeliaceae) are terrestrial herbs with a centre of diversity in the central South American Andes. To resolve infra- and intergeneric relationships among Fosterella and their putative allies, we conducted a phylogenetic analysis based on sequence data from four chloroplast DNA regions (matK gene, rps16 intron, atpB-rbcL and psbB-psbH intergenic spacers). Sequences were generated for 96 accessions corresponding to 60 species from 18 genera. Among these, 57 accessions represented 22 of the 31 recognized Fosterella species and one undescribed morphospecies. Maximum parsimony and Bayesian inference methods yielded well-resolved phylogenies. The monophyly of Fosterella was strongly supported, as was its sister relationship with a clade comprising Deuterocohnia, Dyckia and Encholirium. Six distinct evolutionary lineages were distinguished within Fosterella. Character mapping indicated that parallel evolution of identical character states is common in the genus. Relationships between species and lineages are discussed in the context of morphological, ecological and biogeographical data as well as the results of a previous amplified fragment length polymorphism (AFLP) study.