The relationship between inter- and intra-specific aggression

Some evidence on the motivational relationship between aggressive behaviour towards conspecifics, predators and potential prey is discussed. This does not support the suggesstion that these always depend on distict internal factors. Various selection pressures are considered which may well result in motivational links between the different patterns of aggressive behaviour.     

A direct comparison between the genetic maps of sorghum and rice

A direct comparison of the genetic linkage maps of sorghum and rice is proposed. It is based on the mapping of a common set of 123 RFLP probes scattered on the genomes of both species. For each species a composite map was established by merging two individual maps comprising many common loci. This enabled us to confirm the global correspondence scheme that had previously been established between the chromosomes of sorghum and rice. It also provided a more detailed insight into the conservation of synteny and colinearity: 69% of the loci mapped on a given rice chromosome mapped to the corresponding homoeologous chromosome in sorghum; among them, 84% formed a colinear arrangement between the two species. Local inversions and translocations were detected. Received: 27 April 2000 / Accepted: 26 May 2000     

Alignment of genetic and physical maps of Gibberella zeae

We previously published a genetic map of Gibberella zeae (Fusarium graminearum sensu lato) based on a cross between Kansas strain Z-3639 (lineage 7) and Japanese strain R-5470 (lineage 6). In this study, that genetic map was aligned with the third assembly of the genomic sequence of G. zeae strain PH-1 (lineage 7) using seven structural genes and 108 sequenced amplified fragment length polymorphism markers. Several linkage groups were combined based on the alignments, the nine original linkage groups were reduced to six groups, and the total size of the genetic map was reduced from 1,286 to 1,140 centimorgans. Nine supercontigs, comprising 99.2% of the genomic sequence assembly, were anchored to the genetic map. Eight markers (four markers from each parent) were not found in the genome assembly, and four of these markers were closely linked, suggesting that >150 kb of DNA sequence is missing from the PH-1 genome assembly. The alignments of the linkage groups and supercontigs yielded four independent sets, which is consistent with the four chromosomes reported for this fungus. Two proposed heterozygous inversions were confirmed by the alignments; otherwise, the colinearity of the genetic and physical maps was high. Two of four regions with segregation distortion were explained by the two selectable markers employed in making the cross. The average recombination rates for each chromosome were similar to those previously reported for G. zeae. Despite an inferred history of genetic isolation of lineage 6 and lineage 7, the chromosomes of these lineages remain homologous and are capable of recombination along their entire lengths, even within the inversions. This genetic map can now be used in conjunction with the physical sequence to study phenotypes (e.g., fertility and fitness) and genetic features (e.g., centromeres and recombination frequency) that do not have a known molecular signature in the genome.     

Alignment of two genetic linkage maps on porcine chromosome 13

A set of four microsatellite markers from the USDA genetic linkage map of porcine chromosome 13 were mapped in the European Pig Gene Mapping Project (PiGMaP) reference pedigrees. A two-point linkage analysis was performed between these markers and a set of markers known to map to chromosome 13. Pairs of markers that had a lod score greater than three were used to construct a multi-point linkage map, permitting alignment of the United States Department of Agriculture (USDA) map to the PiGMaP.     

Differential inter- and intra-specific defense induction in Lupinus by Myzus persicae feeding

Experiments were conducted to investigate the potential induction of plant defenses by Myzus persicae Sulzer (Homoptera: Aphididae) feeding on five lupin, Lupinus spp. (Leguminosae), varieties with well‐characterized levels of aphid resistance. Myzus persicae feeding on L. angustifolius and L. luteus varieties induced genotype‐specific changes in their host that were not consistent with the level of aphid resistance or the plant species. The plant responses were systemically detected by apterous and alate forms of the aphids. Chemical assays revealed no induction of oxidizing enzyme (catalase, peroxidase, or polyphenol oxidase) activity, serine or cystein proteinase inhibitors, or soluble phenolics in any of the five varieties tested following 3 days of feeding by 10 or 30 aphids. However, there were significant differences among the five lupin varieties in the levels of peroxidase and polyphenol oxidase activity, proteinase inhibitors, and soluble phenolics.     

Analysis of inter- and intra-specific competition amongst intertidal limpets with different methods of feeding

Summary The prosobranch limpet Cellana tramoserica grazes on microalgae, including the spores of macroalgae, and coexists with the pulmonate limpets Siphonaria denticulata and S. virgulata at mid-tidal levels on sandstone shores in New South Wales. These siphonarians graze on macroalgae, leaving the basal parts of the thalli intact. Where Cellana graze, they are capable of removing all algae; where Siphonaria graze, they leave at least a thin film of alga on the rocks, which is available to Cellana. S. denticulata normally show invariant homing behaviour, whereas S. virgulata tend to move around at random when Cellana are present, but apparently home when Cellana are absent. Both siphonarians have been observed to show opportunistic behavioural responses by moving towards patches of macroalgal foods when they become available.Experimental ecclosures of limpets at different densities and in different combinations revealed that Cellana tramoserica suffered increased mortality and reduced growth due to intraspecific competition when at increased densities. There was no effect on Cellana of increased densities of either species of Siphonaria. Nor was there any interspecific interaction between the siphonarians. Both species of Siphonaria showed some reduction of growth at increased intraspecific density. More importantly, both showed increased mortality when enclosed with low densities of Cellana. Larger densities of Cellana had no effect; the numbers of Cellana could not be maintained because of the reductions caused by intraspecific competition. Even after 27 weeks in enclosures with Cellana, the numbers of Siphonaria never declined to zero in any experimental enclosure. Thus, Cellana has a competitive effect on the survival of siphonarian limpets, but is unable to exclude them from an area of the shore. Siphonaria spp., in contrast, have no effect on Cellana.The nature of the competitive interactions between these types of limpets is explaied in terms of their methods of feeding; Cellana can exploit the food-resource before it reaches a suitable size for Siphonaria. The coexistence of Siphonaria spp. with Cellana is discussed with respect to the behaviour of the pulmonates. Intraspecific competition leading to reduced densitities of Cellana, however, will ensure that Cellana cannot exploit all the food resources, and some will be available to Siphonaria. The consequences of inter- and intra-specific competition among grazing gastropods are discussed with reference to the structure of intertidal communities, and it appears that competition for food is fundamentally different from competitive interactions for space in the organization of such communities.     

Mapping of neural crest pathways in Xenopus laevis using inter- and intra-specific cell markers

This study examines the pathways of migration followed by neural crest cells in Xenopus embryos using two recently described cell marking techniques. The first is an interspecific chimera created by grafting Xenopus borealis cells into Xenopus laevis hosts. The cells of these closely related species can be distinguished by their nuclear dimorphism. The second type of marker is created by microinjection of lysinated dextrans into fertilized eggs which can then be used for intraspecific grafting. These recently developed fluorescent dyes are fixable and identifiable in both living and fixed embryos. After grafting labeled donor neural tubes into unlabeled host embryos, the distribution of neural crest cells at various stages after grafting was used to define the pathways of neural crest migration. To control for possible grafting artifacts, fluorescent lysinated dextran was injected into a single blastomere which gives rise to a large number of neural crest cells, thereby labeling the neural crest without grafting. By all three techniques, Xenopus neural crest cells were observed along two predominant pathways in the trunk. The majority of neural crest cells were observed along a "ventral" route, between the neural tube and somite, the notochord and somite, and along the dorsal mesentery. A second group of neural crest cells was observed "dorsally" where they populated the dorsal fin. A third minor "lateral" pathway was observed primarily in borealis/laevis chimerae and in blastomere-injected embryos; some neural crest cells were observed underneath the ectoderm lateral to the neural tube. Along the rostrocaudal axis, neural crest cells were not continuously distributed but were primarily located across from the caudal two-thirds of the somite. Fewer than 3% of the neural crest cells were observed across from the rostral third of each somite. When grafted to ventral locations, neural crest cells were not able to migrate dorsally but migrated laterally along the dorsal mesentery. Labeled neural crest cells gave rise to cells of the spinal, sympathetic, and enteric ganglia as well as to adrenal chromaffin cells, Schwann cells, pigment cells, mesenchymal cells of the dorsal fin, and some cells in the integuments and in the region of the pronephros. These results show that the neural crest migratory pathways in Xenopus differ from those in the avian embryo. In avians NC cells migrate as a closely associated sheet of cells while in Xenopus they migrate as individual cells. Both species exhibit a metamerism in the neural crest cell distribution pattern along the rostrocaudal axis.(ABSTRACT TRUNCATED AT 400 WORDS)     

Correlation between thermal stability maps and genetic maps of double-stranded DNAs

The positional correlation of boundaries of cooperatively melting regions with boundaries of genes and with cleavage sites of restriction enzymes are statistically examined for phiX174, G4, fd, SV40, BKV, and polyoma DNAs. A statistically significant correlation does exist in the case of gene boundaries, but none is detected for cleavage sites.     

Single primer amplification reaction (SPAR) reveals inter- and intra-specific natural genetic variation in five species of Cymbidium (Orchidaceae)

A total of 53 primers belonging to three SPAR methods, viz. RAPD, ISSR and DAMD, collectively produced 456 polymorphic amplicons with 96.6% polymorphism at inter-specific level in five species of Cymbidium, viz. C. aloifolium, C. mastersii, C. elegans, C. eburneum and C. tigrinum, whereas at intra-specific level, the observed polymorphism ranged from 51.2% to 77.1% among them. Three SPARs collectively revealed 25 unique species-specific amplicons; most of them were amplified with RAPD and DAMD primers besides few bands which were either missed (absent) or lost (heterozygosity). UPGMA clustering evidently distinguished the representatives of C. aloifolium and C. tigrinum, with distinct genetic distance, which may be due to their entirely different habitats as well as discrete morphological characteristics. Upon analysis of the data generated, all the three SPAR methods, either independently and/or in combination, revealed wide range of genetic variation between and within five species of Cymbidium. Comparison of matrix of individual SPAR method revealed that analysis of natural genetic variation using combination of SPAR methods, rather than an isolated approach, is highly effective. The critical analyses of the amplicon data are indicative of DAMD as the most powerful SPAR method by showing highest resolving power (Rp) followed by ISSR and RAPD. Alternatively, the total polymorphic information content was highest in case of RAPD followed by other two SPAR methods. Thus, the present investigation for the first time provides a valuable baseline data for genetic variation at inter- and intra-specific levels in horticultural Cymbidiums and also addresses conservation concerns.     

Linking limitation to species composition: importance of inter- and intra-specific variation in grazing resistance

Short-term responses of producers highlight that key nutrients (e.g., N, P)—or combinations of these nutrients—limit primary production in aquatic and terrestrial ecosystems. These discoveries continue to provide highly valuable insights, but it remains important to ask whether nutrients always predominantly limit producers despite wide variation in nutrient supply and herbivory among systems. After all, predictions from simple food chain models (derived here) readily predict that limitation by grazers can exceed that by nutrients, given sufficient enrichment. However, shifts in composition of producers and/or increasing dominance of invulnerable stages of a producer can, in theory, reduce grazer limitation and retain primacy of nutrient limitation along nutrient supply gradients. We observed both mechanisms (inter- and intra-species variation in vulnerability to herbivory) working in a two-part mesocosm experiment. We incubated diverse benthic algal assemblages for several months either in the presence or absence of benthic macro-grazers in mesocosms that spread a broad range of nutrient supply. We then conducted short-term assays of nutrient and grazer limitation on these communities. In the “historically grazed” assemblages, we found shifts from more edible, better competitors to more resistant producers over enrichment gradients (as anticipated by the food web model built with a tradeoff in resistance vs. competitive abilities). However, contrary to our expectations, “historically ungrazed” assemblages became dominated by producers with vulnerable juvenile forms but inedible adult forms (long filaments). Consequently, we observed higher resource limitation rather than grazer limitation over this nutrient supply gradient in both “historically grazed” (expected) and “historically ungrazed” (not initially expected). Thus, via multiple, general mechanisms involving resistance to grazing (changes in species composition or variation in stage-structured vulnerability), producer assemblages should remain more strongly or as strongly limited by nutrients than grazers, even over large enrichment gradients. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Potential of (GATA)n microsatellites from rice for inter- and intra-specific variability studies

Background

The microsatellite, (GATA)_n has been frequently used for DNA fingerprinting. However, very few attempts have been made to analyze (GATA)_n-containing loci in rice.

Results

Three polymorphic (GATA)_n-harboring loci viz. OS1A6, OS1H10 and OS2E7, containing 7–13 repeat motifs were identified from a genomic library of a cultivated rice, Oryza sativa var. Basmati-370 using oligonucleotide probe (GATA)₄. When (GATA)_n flanking primers were used to screen 26 wilds (representing different genomes of rice), 16 cultivars, 47 Indian elite rice varieties and 37 lines resistant/susceptible to bacterial blight, up to 22 alleles were obtained at an individual locus. Also, interestingly the bacterial blight resistant lines clustered into a separate group from the remaining rice genotypes, when a dendrogram was constructed based on the polymorphism obtained at the three loci. This may be due to the partial homology of the clones OS1H10 and OS2E7 to regions encoding O. longistaminata receptor kinase-like protein and pathogenesis-related protein. The ability of these O. sativa flanking primers to amplify DNA of maize, wheat, barley and oat indicates that these (GATA)_n-containing loci are conserved across different cereal genera.

Conclusions

The large allele number obtained reveals the potential of (GATA)_n-containing loci as powerful tools to detect simple sequence length polymorphism (SSLP). The (GATA)_n-flanking primers were not only useful in distinguishing between closely related genotypes, but could also be used for cross-species amplification and are also conserved across different cereal genera. These loci could also cluster the bacterial blight resistant/susceptible lines into different groups based on the resistance genes present in them.     

Comparison of molecular linkage maps and QTLs for morphological traits in two reciprocal backcross populations of rice

Comparison of maps and QTLs between populations may provide us with a better understanding of molecular maps and the inheritance of traits. We developed and used two reciprocal BC1F1 populations, IP/DS//IP and IP/DS//DS, for QTL analysis. DS (Dasanbyeo) is a Korean tongil-type cultivar (derived from an indica x japonica cross and similar to indica in its genetic make-up) and IP (Ilpumbyeo) is a Korean japonica cultivar. We constructed two molecular linkage maps corresponding to each backcross population using 196 markers for each map. The length of each chromosome was longer in the IP/DS//IP population than in the IP/DS//DS population, indicating that more recombinants were produced in the IP/DS//IP population. Distorted segregation was observed for 44 and 19 marker loci for the IP/DS//IP and IP/DS//DS populations, respectively; these were mostly skewed in favor of the indica alleles. A total of 36 main effect QTLs (M-QTLs) and 15 digenic epistatic interactions (E-QTLs) were detected for the seven traits investigated. The phenotypic variation explained (PVE) by M-QTLs ranged from 3.4% to 88.2%. Total PVE of the M-QTLs for each trait was significantly higher than that of the E-QTLs. The total number of M-QTLs identified in the IP/DS//IP population was higher than in the IP/DS//DS population. However, the total PVE by the M-QTLs and E-QTLs together for each trait was similar in the two populations, suggesting that the two BC1F1 populations are equally useful for QTL analysis. Maps and QTLs in the two populations were compared. Eleven new QTLs were identified for SN, SF, GL, and GW in this study, and they will be valuable in marker-assisted selection, particularly for improving grain traits in tongil-type varieties.     

Alignment of optical maps.

We introduce a new scoring method for calculation of alignments of optical maps. Missing cuts, false cuts, and sizing errors present in optical maps are addressed by our alignment score through calculation of corresponding likelihoods. The size error model is derived through the application of Central Limit Theorem and validated by residual plots collected from real data. Missing cuts and false cuts are modeled as Bernoulli and Poisson events, respectively, as suggested by previous studies. Likelihoods are used to derive an alignment score through calculation of likelihood ratios for a certain hypothesis test. This allows us to achieve maximal descriminative power for the alignment score. Our scoring method is naturally embedded within a well known DP framework for finding optimal alignments.     

SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum

We present SSR-based genetic maps from a cross between Miscanthus sacchariflorus Robustus and M. sinensis, the progenitors of the promising cellulosic biofuel feedstock Miscanthus × giganteus. cDNA-derived SSR markers were mapped by the two-way pseudo-testcross model due to the high heterozygosity of each parental species. A total of 261 loci were mapped in M. sacchariflorus, spanning 40 linkage groups and 1,998.8 cM, covering an estimated 72.7% of the genome. For M. sinensis, a total of 303 loci were mapped, forming 23 linkage groups and 2,238.3 cM, covering 84.9% of the genome. The use of cDNA-derived SSR loci permitted alignment of the Miscanthus linkage groups to the sorghum chromosomes, revealing a whole genome duplication affecting the Miscanthus lineage after the divergence of subtribes Sorghinae and Saccharinae, as well as traces of the pan-cereal whole genome duplication. While the present maps provide for many early research needs in this emerging crop, additional markers are also needed to improve map density and to further characterize the structural changes of the Miscanthus genome since its divergence from sorghum and Saccharum.     

Inter and intra-specific genetic variability of oral Candida species

In this report, strains of five different Candida species (Candida albicans, Candida guilliermondii, Candida tropicalis, Candida krusei, and Candida parapsilosis) isolated from healthy human oral cavities as well as their respective type-strains were used in order to establish the genetic diversity existing among the different species and within a certain species, by the analysis of their electrophoretic alloenzyme patterns. These profiles were analyzed for their band positions in the gels, which allowed to group the strains of the same species in species-specific clusters and to treat them as conspecific populations. A total of thirteen enzymatic loci were obtained (ACO, ADH1, ADH2, CAT, G6PDH, GDH, GOT, IDH1, IDH2, LAP, LDH, PER, and SOD). The allelic frequencies (p) and the heterozygosity (h) for all the thirteen loci were determined by diversity index formulas. The GST index is the estimated proportion of genetic diversity that was applied in order to establish inter and intra populational diversity, which, for our results, indicated that 37.75% of total genetic diversity was attributable to differences among the species and the remaining 62.25% was attributable to differences within these populations. An Euclidian distance dendrogram for the different conspecific populations was built, showing that C. guilliermondii grouped first with C. tropicalis and thus formed a expanded cluster with C. albicans. This cluster combined later with another one composed by C. parapsilosis and C. krusei. Comparing our results to the others that were obtained by different molecular techniques, we have observed that the clustering hierarchies follow different paths of organization, varying according to the methodology employed.     

Comparison between Poncirus and Citrus genetic linkage maps

Five genetic linkage maps were constructed for the parents of three progenies: Citrus aurantium (A) x Poncirus trifoliata var. Flying Dragon (Pa), C. volkameriana (V) x P. trifoliata var. Rubidoux (Pv) and a self-pollination of P. trifoliata var. Flying Dragon (Pp). The number of polymorphic markers assayed ranged from 48 for Pa to 120 for A according to the heterozygosity of each parental. As our focus was on genome comparison, most of the markers were newly generated simple sequence repeats. Inter-retrotransposon amplified polymorphisms based on four retrotransposon sequences isolated from Citrus spp were also used to saturate the maps. These polymorphisms were much more frequent in A (53) than in Pa (15) and randomly distributed throughout both genomes. Since comparative genomics and quantitative trait locus analysis applicability depends on the reliability of marker ordering, the causes of variation in marker order were investigated. Around 25% of the markers showed gametal segregation distortions. Segregation distortions were also observed at the zygotic level towards a reduction in the observed frequency of homozygotes from that expected in linkage groups 5 and 7. The presence of balanced lethal factors or gametal incompatibility genes in those genomic regions would explain a zygotic advantage of heterozygotes at these specific regions. Four differences in genomic organization were observed; three are putative translocations and affect homeologous linkage groups 3, 7 and 11, where highly distorted markers are found. Other causes of variation in marker order are also discussed: the introduction of new markers in the map, lowering the LOD score and the mapping software. These results represent the first comparative mapping analysis among Citrus and Poncirus species.     

Correlation between genetic and cytogenetic maps of the rat

To correlate rat genetic linkage maps with cytogenetic maps, we localized 25 new cosmid-derived simple sequence length polymorphism (SSLP) markers and 14 existing genetic markers on cytogenetic bands of chromosomes, using fluorescence in situ hybridization (FISH). Next, a total of 58 anchor loci, consisting of the 39 new and 19 previously reported ones, were integrated into the genetic linkage maps. Since most of the new anchor loci were developed to be localized near the terminals of the genetic or cytogenetic maps for each chromosome, the orientation and coverage of the whole genetic linkage maps were determined or confirmed with respect to the cytogenetic maps. Thus, we provide here a new base for rat genetic maps. Received: 9 September 1997 / Accepted: 11 November 1997     

水位波动对南美蟛蜞菊和蟛蜞菊种内及种间关系的影响

以外来入侵植物南美蟛蜞菊和本地近缘种蟛蜞菊为对象,通过温室模拟3种水位波动模式(水位无波动,水位波动模式分别为15 cm-0 cm-15 cm和0 cm-15 cm-0 cm)交叉5种定植模式(试验容器内分别为入侵种单株、本土种单株、入侵种6株、本土种6株以及2物种各3株混种)的试验,研究水位波动对入侵植物和本地近缘种生长繁殖性状及种内种间相互作用的影响.结果表明: 水位波动显著降低了南美蟛蜞菊和蟛蜞菊的总生物量、茎生物量、叶生物量、根生物量、茎长、节点数、叶片数及叶面积,对南美蟛蜞菊和蟛蜞菊种内及种间竞争系数的影响均显著.水位波动改变了南美蟛蜞菊的种内和种间竞争关系,说明入侵植物南美蟛蜞菊对水位波动更为敏感,对环境改变表现出更强的适应性.     

The application of high-density genetic maps of rye for the detection of QTLs controlling morphological traits

The development of genetic maps is, nowadays, one of the most intensive research activities of plant geneticists. One of the major goals of genome mapping is the localisation of quantitative trait loci (QTLs). This study was aimed at the identification of QTLs controlling morphological traits of rye and comparison of their localisation on genetic maps constructed with the use of genetically different germplasms. For QTL analyses, two high-density consensus maps of two populations (RIL-S and RIL-M) of recombinant inbred lines (RIL) were applied. Plant height (Ph), length of spikes (Sl) and the number of spikelets per spike (Sps) were studied in both populations. Additionally, the number of kernels per spike under isolation (Kps), the weight of kernels per spike (Kw) and thousand kernel weight (Tkw) were assessed in the RIL-M population. Except for Tkw, the majority of the traits were correlated to each other. The non-parametric Kruskal–Wallis (K-W) test and composite interval mapping (CIM) revealed 18/48 and 24/18 regions of rye chromosomes engaged in the determination of Ph, Sl and Sps in the RIL-S and RIL-M populations, respectively. An additional 18/15 QTLs controlling Kps, Kw and Tkw were detected on a map of the RIL-M population. A numerous group of QTLs detected via CIM remained in agreement with the genomic regions found when the K-W test was applied. Frequently, the intervals indicated by CIM were narrower.     

Assessment of inter- and intra-specific variability in the main species of Boletus edulis complex by ITS analysis

The Boletus edulis species complex includes ectomycorrhizal fungi producing edible mushrooms appreciated worldwide. However, species delineation is very difficult in these fungi, because it is based exclusively on a few, highly variable morphological features. As a consequence, a high number of taxa--including several varieties, subspecies and/or species sensu stricto--have been described in this species complex. In this paper we report on an extensive analysis of internal transcribed spacer of the nuclear rDNA region on a large sample of species of the B. edulis complex, mainly harvested in Italy, and representative of the European variability of this group. The molecular analysis allowed us to discriminate among and within B. edulis, B. aestivalis, B. pinophilus and B. aereus spp. and resolve their phylogenetic relationship.