Blurry artifacts: a retraction

Abstract. This note is to apologize for an error in the computer program used to evaluate the random data used in Fuzzy Set Ordination according to Zhang & Oxley. After correction of this error no artifacts could be detected any longer. However, the basic conclusion of the earlier critical note still stands: if one selects environmental variables after analyzing the results of a multivariate gradient analysis, and then uses these variables as input into a multiple univariate gradient analysis, the results are expected to be comparable.     

Molecular genetic characterization of plant somatic hybrids

An efficient and easy method for genetic characterization of plant somatic hybrids is proposed. In a first qualitative approach, four somatic hybrids and their parental species (Nicotiana tabacum andN. plumbaginifolia) were characterized by DNA fingerprinting and Random Amplification of Polymorphic DNA (RAPD). After this, a quantitative estimation of the degree of parental contribution to the hybrids was carried out by means of a slot-blot analysis. Both qualitative methods, showed one hybrid identical toN. tabacum, two almost identical toN. plumbaginifolia, and a fourth similar to this parental species, but with someN. tabacum admixture. The quantitative method, for the same hybrids, gave 83%, 7%, 7%, and 37%N. tabacum DNA contribution, respectively.     

The upper cretaceousLacazina limestone in the Basco-Cantabrian and Iberian basins of northern Spain: Cold-water grain associations in warm-water environments

Summary The Upper Santonian to Lower CampanianLacazina Limestone consists of massive, often amalgamated beds of packstones and grainstones which were deposited in a shallow marine environment. The most abundant skeletal components are miliolid foraminifera, echinoderm, bivalve and bryozoan fragments, peloids and sparse red algae. Small, solitary corals only occur sporadically. Hermatypic corals, sponges and green algae are missing. The series which reaches thicknesses between 60 m and 160 m, was sampled at intervals of 0.5 m at five localities. The petrographic features throughout the series are mainly a product of changing depositional energy. The limestones are well cemented. Diagenesis is characterized by a transition from marine phreatic to burial cementation. Syntaxial and blocky calcite cements predominate over early acicular to bladed and microgranular cements. The faunal association within theLacazina Limestone exhibits features typical for temperate water i.e.foramol carbonates. On the other hand, oxygen (δ¹⁸O =-1.7 to −6.3 ‰ PDB) and carbon (δ¹³C to 3.0‰ PDB) isotope values of diagentically unaltered bivalve shells indicate warm surface waters corresponding better to the palaeogeographical situation of theLacazina Limestone. Nutrient-surplus is proposed as a limiting factor preventing the development of reefs and finally ofchlorozoan sediments. In the sense of sequence stratigraphy, theLacazina Limestone is interpreted to contain transgressive and highstand systems tracts. This interpretation fits well into theHaq-Vail-curve. The series shows no visible high-frequency cyclicity in the field. Several cycles were found by means of principle component analysis and spectral analysis. Their relationships to the Milankovitch spectrum are discussed. The ammonite fauna of the unit and of preceding sediments (late Coniacian to early Campanian) is described and some inoceramids are figured. They permit—for the first time—the exact dating of theLacazina Limestone in the Basco-Cantabrian Basin (BCB) and throw light on a prominent faunal change at the Coniacian/Santonian boundary. The Cenomanian to Coniacian ammonite faunas which were dominated by endemic Tethyan pseudoceratitic faunas are replaced by cosmopolitan species dominated by Madagascan elements. This drastic change permits speculations about the installation of a new oceanic current system in the Santonian.     

Composition and dynamics of epilithic algae in a forest stream at Shillong (India)

The seasonal dynamics of epilithic algae in a third order pristine forest stream were analyzed over a period of 2 years. Stream water was slightly acidic and nutrient poor. Encrusting, filamentous flocs, and filaments were found. Algal standing crop was high (mean concentration of Chl a 16–43 mg m^–2) in spring. Filamentous algae contributed most to standing crop. Diatoms made up over 85% by number of the epilithon. Blue-greens were abundant upstream, and chlorophytes downstream. This shift was ascribed to greater light availability downstream. The community was more diverse during spring. Water current was the most important variable regulating epilithon structure. Total phosphorus (TP), orthophosphate (O-PO _inf4 ^su3– ), silica (Si⁴⁺), nitrate (NO _inf3 ^su– ) and conductance correlated negatively with flow rate. Green algae showed a positive correlation to phosphorus during low and stable flow. During rapid runoff, diatoms were the most resistant forms. Seasonal change in the epilithic community was mainly regulated by fluctuations in flow rate.     

Use of random amplified polymorphic DNA (RAPD) markers in the discrimination and verification of genotypes in Eucalyptus

We carried out four separate studies using random amplified polymorphic DNA (RAPD) markers to analyse samples of Eucalyptus supplied by several different organisations. The objective was to examine the reproducibility of the RAPD technique and its ability to discriminate between individual genotypes for verification of clonal identities. We found that RAPD profiles that are unique to a genotype can be generated reliably and simply and that even closely related genotypes can be distinguished. In addition, in each of the four studies, we detected cases where the plant material studied had been mis-sampled or mis-labelled (i.e. the RAPD profiles were not consistent with the identification numbers): (1) ramets of a Eucalyptus grandis clone were found to be derived from 2 different clones; (2) ramets labelled as 2 different Eucalyptus hybrid clones were found to be the same clone, owing to a mis-planted clonal hedge; (3) samples supplied as a single progeny of a controlled E. nitens cross were derived from two crosses involving different pairs of parents; (4) mis-labelling was detected for ramets of 4 of a set of 10 clones of E. grandis and E. camaldulensis. For three of the four studies, the detection of genotype mis-identifications was unexpected, suggesting that labelling or sampling errors during the handling of plant material are a frequent occurrence, with potentially serious economic consequences.     

Molecular markers shared by diverse apomictic Pennisetum species

Two molecular markers, a RAPD (randomly amplified polymorphic DNA) and a RFLP/STS (restriction fragment length polymorphism/sequence-tagged site), previously were found associated with apomictic reproductive behavior in a backcross population produced to transfer apomixis from Pennisetum squamulatum to pearl millet. The occurrence of these molecular markers in a range of 29 accessions of Pennisetum comprising 11 apomictic and 8 sexual species was investigated. Both markers were specific for apomictic species in Pennisetum. The RFLP/STS marker, UGT 197, was found to be associated with all taxa that displayed apomictic reproductive behavior except those in section Brevivalvula. Neither UGT197 nor the cloned RAPD fragment OPC-04₆₀₀ hybridized with any sexually reproducing representatives of the genus. The cloned C04₆₀₀ was associated with 3 of the 11 apomictic species, P. ciliare, P. massaicum, and P. squamulatum. UGT197 was more consistently associated with apomictic reproductive behavior than OPC04₆₀₀ or cloned C04₆₀₀, thus it could be inferred that UGT197 is more closely linked to the gene(s) for apomixis than the cloned C04₆₀₀. The successful use of these probes to survey other Pennisetum species indicates that apomixis is a trait that can be followed across species by using molecular means. This technique of surveying species within a genus will be useful in determining the relative importance of newly isolated markers and may facilitate the identification of the apomixis gene(s).     

A genetic linkage map of Picea abies Karst., based on RAPD markers,as a tool in population genetics

Norway spruce (Picea abies Karst.) is a most important species among European forest trees for both economical and ecological reasons. However, this species has suffered from a lack of information on the genetic side due to the scarcity of linkage data. In this study we have used a population of 72 megagametophytes from a single tree in a natural Italian stand to produce a genetic linkage map by means of RAPD markers. Ninety-six random decamers used as primers yielded 185 polymorphic loci showing Mendelian inheritance. Analysis of the segregation by multipoint analysis allowed us to define 17 major linkage groups covering a total distance of 3584 cM, with an average spacing between markers of 22 cM. Possible uses of a genetic linkage map with respect to population ecology and genetics are discussed.     

Identification and localization of molecular markers linked to the Lr9 leaf rust resistance gene of wheat

Near-isogenic lines (NILs) for the leaf rust resistance gene Lr9 were screened for polymorphisms at the molecular level. RAPD (random amplified polymorphic DNA) primers as well as RFLP (restriction fragment length polymorphism) markers were used. Out of 395 RAPD primers tested, three showed polymorphisms between NILs, i.e., an additional band was found in resistant lines. One of these polymorphic bands was cloned and sequenced. Specific primers were synthesized, and after amplification only resistant lines showed an amplified product. Thus, these primers define a sequence-tagged site that is specific for the translocated fragment carrying the Lr9 gene. A cross between a resistant NIL and the spelt (Triticum spelta) variety Oberkulmer was made, and F₂ plants were analyzed for genetic linkage. All three polymorphisms detected by the PCR (polymerase chain reaction) and one RFLP marker (cMWG684) showed complete linkage to the Lr9 gene in 156 and 133 plants analyzed, respectively. A second RFLP marker (PSR546) was closely linked (8±2.4 cM) to the Lr9 gene and the other four DNA markers. As this marker maps to the distal part of the long arm of chromosome 6B of wheat, Lr9 and the other DNA markers also map to the distal region of 6BL. All three PCR markers detected the Lr9 gene in independently derived breeding lines and varieties, thus proving their general applicability in wheat breeding programs.     

Inheritance of restriction fragment length polymorphisms and random amplified polymorphic DNAs in coastal Douglas-fir

A total of 225 new genetic loci [151 restriction fragment length polymorphisms (RFLP) and 74 random amplified polymorphic DNAs (RAPD)] in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] have been identified using a three-generation outbred pedigree. The Mendelian inheritance of 16 RFLP loci and 29 RAPD loci was demonstrated based on single-locus segregation in a sample of F₂ progeny. One RFLP locus, PtIFG2025, showed segregation distortion. Probe pPtIFG2025 is a loblolly pine cDNA probe encoding for rbcS. The 16 RFLP loci and 23 allozyme loci were also assayed in a sample of 16 Douglas-fir seed-orchard clones. Allelism was determined at 11 of the 16 RFLP loci. RFLPs were able to detect slightly more variation (4.0 alleles per locus) than allozymes (3.1 alleles per locus). The inheritance of an additional 80 RAPD loci was determined based on haploid segregation analysis of megagametophytes from parent tree 013-1. Once 200–300 markers are identified and placed on a genetic map, quantitative trait loci affecting bud phenology will be mapped.     

Linkage analysis of sex determination in the honey bee (Apis mellifera)

A colony-level phenotype was used to map the major sex determination locus (designatedX) in the honey bee (Apis mellifera). Individual queen bees (reproductive females) were mated to single drones (fertile males) by instrumental insemination. Haploid drone progeny of an F1 queen were each backcrossed to daughter queens from one of the parental lines. Ninety-eight of the resulting colonies containing backcross progeny were evaluated for the trait low brood-viability resulting from the production of diploid drones that were homozygous atX. DNA samples from the haploid drone fathers of these colonies were used individually in polymerase chain reactions (PCR) with 10-base primers. These reactions generated random amplified polymorphic DNA (RAPD) markers that were analyzed for cosegregation with the colony-level phenotype. One RAPD marker allele was shared by 22 of 25 drones that fathered low brood-viability colonies. The RAPD marker fragment was cloned and partially sequenced. Two primers were designed that define a sequence-tagged site (STS) for this locus. The primers amplified DNA marker fragments that cosegregated with the original RAPD marker. In order to more precisely estimate the linkage betweenX and the STS locus, another group of bees consisting of progeny from one of the low-brood viability colonies was used in segregation analysis. Four diploid drones and 181 of their diploid sisters (workers, nonfertile females) were tested for segregation of the RAPD and STS markers. The cosegregating RAPD and STS markers were codominant due to the occurrence of fragment-length alleles. The four diploid drones were homozygous for these markers but only three of the 181 workers were homozygotes (recombinants). Therefore the distance betweenX and the STS locus was estimated at 1.6 cM. An additional linked marker was found that was 6.6 cM from the STS locus.