More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy

The relative contribution of taxon number and gene number to accuracy in phylogenetic inference is a major issue in phylogenetics and of central importance to the choice of experimental strategies for the successful reconstruction of a broad sketch of the tree of life. Maximization of the number of taxa sampled is the strategy favored by most phylogeneticists, although its necessity remains the subject of debate. Vast increases in gene number are now possible due to advances in genomics, but large numbers of genes will be available for only modest numbers of taxa, raising the question of whether such genome-scale phylogenies will be robust to the addition of taxa. To examine the relative benefit of increasing taxon number or gene number to phylogenetic accuracy, we have developed an assay that utilizes the symmetric difference tree distance as a measure of phylogenetic accuracy. We have applied this assay to a genome-scale data matrix containing 106 genes from 14 yeast species. Our results show that increasing taxon number correlates with a slight decrease in phylogenetic accuracy. In contrast, increasing gene number has a significant positive effect on phylogenetic accuracy. Analyses of an additional taxon-rich data matrix from the same yeast clade show that taxon number does not have a significant effect on phylogenetic accuracy. The positive effect of gene number and the lack of effect of taxon number on phylogenetic accuracy are also corroborated by analyses of two data matrices from mammals and angiosperm plants, respectively. We conclude that, for typical data sets, the number of genes utilized may be a more important determinant of phylogenetic accuracy than taxon number.     

Discovery and characterization of a large number of diagnostic markers to discriminate Oncorhynchus mykiss and O. clarkii

Hybridization of cutthroat trout and steelhead/rainbow trout is ubiquitous where they are sympatric, either naturally or owing to introductions. The ability to detect hybridization and introgression between the two species would be greatly improved by the development of more diagnostic markers validated across the two species' many phylogenetic lineages. Here, we describe 81 novel genetic markers and associated assays for discriminating the genomes of these sister species. These diagnostic nucleotide polymorphisms were discovered by sequencing of rainbow trout expressed sequence tags (ESTs) in a diverse panel of both cutthroat trout and steelhead/rainbow trout. The resulting markers were validated in a large number of lineages of both species, including all extant subspecies of cutthroat trout and most of the lineages of rainbow trout that are found in natural sympatry with cutthroat trout or used in stocking practices. Most of these markers (79%) distinguish genomic regions for all lineages of the two species, but a small number do not reliably diagnose coastal, westslope and/or other subspecies of cutthroat trout. Surveys of natural populations and hatchery strains of trout and steelhead found rare occurrences of the alternative allele, which may be due to either previous introgression or shared polymorphism. The availability of a large number of genetic markers for distinguishing genomic regions originating in these sister species will allow the detection of both recent and more distant hybridization events, facilitate the study of the evolutionary dynamics of hybridization and provide a powerful set of tools for the conservation and management of both species.     

Chromosome number and DNA ploidy level reports of vascular plants — 4

Section Botany

Chromosome number and DNA ploidy level reports of vascular plants — 4     

Influence of melatonin and serotonin on the number of rat pineal “synaptic” ribbons and spherules in vitro

Summary Previous studies have shown that the synaptic ribbons (SR) and spherules (SS) of the mammalian pineal gland may respond differently under physiological and various experimental conditions. The aim of the present study was to gain insight into the mechanisms that may be responsible for the numerical changes of these organelles during a 24-h cycle. As the possibility exists that the structures are influenced by substances synthesized within the pinealocyte, rat pineal glands were cultured with and without added melatonin or serotonin, using an experimental protocol such that the addition of melatonin and serotonin mimicks the circadian changes of the respective substances within the pineal. The tissue was processed for electron microscopy and the numbers of SR and SS were counted in a unit area of pineal tissue. The results obtained indicate that melatonin added to the incubation medium increases the number of SR in the first half of the night; serotonin decreases SR numbers in the morning. SS numbers, by contrast, decrease following melatonin administration in the afternoon, and increase in the morning following serotonin administration. It thus appears that the numbers of SR and SS are influenced by melatonin and serotonin and that the two structures are regulated by differential, but nevertheless biochemically closely related mechanisms.Financial support of the Deutsche Forschungsgemeinschaft (Schwerpunktprogramm Neuroendokrinologie, Vo 135/8-4), the Polish Academy of Sciences (Research Program 10.4.04.6), and the Freunde der Universität Mainz e.V. is gratefully acknowledged.On leave from Department of Anatomy, University Medical School, Pécs, Hungary     

Differences in the number of embryonic and pseudo-β-globin genes between HbA and HbB sheep

DNA samples obtained from 8 goats, 1 moufflon, and 84 sheep with HbA, HbAB, and HbB belonging to different breeds were digested withBamHI,EcoRI,HindIII andPstI and probed with the 5 end of the goat ^IV- and ^Z-globin genes. Sheep homozygous for HbA show a different restriction pattern than sheep homozygous for HbB with each of these endonucleases. The main differences is that HbB sheep lack the ^H and ^X genes. These results, in addition to those previously obtained using a probe specific for -globin genes, suggest that HbB sheep probably lack the preadult four-gene set. The DNAs from moufflon and sheep homozygous for HbA show indistinguishable restriction patterns. Furthermore, a number of restriction fragment length polymorphisms (RFLPs) are detected in the ^IV and ^Z DNA regions, and oneHindIII RFLP in the ^VI DNA region.This work was supported by the Ministero della Pubblica Istruzione and, in part, by the Consiglio Nazionale delle Ricerche.     

Viral phylodynamics and the search for an ‘effective number of infections’

Information on the dynamics of the effective population size over time can be obtained from the analysis of phylogenies, through the application of time-varying coalescent models. This approach has been used to study the dynamics of many different viruses, and has demonstrated a wide variety of patterns, which have been interpreted in the context of changes over time in the ‘effective number of infections’, a quantity proportional to the number of infected individuals. However, for infectious diseases, the rate of coalescence is driven primarily by new transmissions i.e. the incidence, and only indirectly by the number of infected individuals through sampling effects. Using commonly used epidemiological models, we show that the coalescence rate may indeed reflect the number of infected individuals during the initial phase of exponential growth when time is scaled by infectivity, but in general, a single change in time scale cannot be used to estimate the number of infected individuals. This has important implications when integrating phylogenetic data in the context of other epidemiological data.     

Mass spectrometry analyses of κ and λ fractions result in increased number of complementarity-determining region identifications

Sera from lung cancer patients contain antibodies against tumor-associated antigens. Specific amino acid sequences of the complementarity-determining regions (CDRs) in the antigen-binding fragment (Fab) of these antibodies have potential as lung cancer biomarkers. Detection and identification of CDRs by mass spectrometry can significantly be improved by reduction of the complexity of the immunoglobulin molecule. Our aim was to molecular dissect IgG into κ and λ fragments to reduce the complexity and thereby identify substantially more CDRs than by just total Fab isolation. We purified Fab, Fab-κ, Fab-λ, κ and λ light chains from serum from 10 stage I lung adenocarcinoma patients and 10 matched controls from the current and former smokers. After purification, the immunoglobulin fragments were enzymatically digested and measured by high-resolution mass spectrometry. Finally, we compared the number of CDRs identified in these immunoglobulin fragments with that in the Fab fragments. Twice as many CDRs were identified when Fab-κ, Fab-λ, κ and λ (3330) were combined than in the Fab fraction (1663) alone. The number of CDRs and κ:λ ratio was statistically similar in both cases and controls. Molecular dissection of IgG identifies significantly more CDRs, which increases the likelihood of finding lung cancer-related CDR sequences.     

Trade-off between seed number and weight: Influence of a grass–endophyte symbiosis

Plant fitness is enhanced by resource allocation to seed number (offspring number) or weight (offspring survival). Besides, there is a well known trade-off in resource allocation between both traits. Symbiotic interactions can influence plant resource allocation to reproduction, yet little research has been performed in this direction. We studied the consequences of a grass–fungus symbiosis on the trade-off between seed number and weight, using Lolium multiflorum and the endophyte Neotyphodium occultans as our study system. In ecological terms, we experimentally removed N. occultans from L. multiflorum plants, and compared reproductive allocation to seed number and weight in endophyte-symbiotic vs. non-symbiotic plants at different levels of nutrient availability (small pots vs. large pots). In evolutionary terms, we compared reproductive allocation between symbiotic vs. non-symbiotic plants for different host genotypes. All plants showed a negative association between seed number and weight, once standardized for total reproductive biomass. Under high nutrient availability, endophyte-symbiotic plants showed higher seed weight than non-symbiotic plants for any seed number. However, no differences were observed under low nutrient availability. Endophyte influence also varied according to L. multiflorum genotype; specifically, endophyte-symbiotic plants showed a lower slope in the relationship between seed number and weight than non-symbiotic plants for the ‘Marshall’ genotype but no endophyte influence was found for the “Pampean” genotype. The results implied a higher plasticity in seed weight and lower plasticity in seed number for symbiotic plants. Indeed, endophyte-symbiotic plants showed an overall lower slope in the association between seed number and total reproductive biomass than non-symbiotic plants. Our results suggest that N. occultans induces heavier seeds in L. multiflorum plants under environmental conditions favorable to plant growth or for certain plant genotypes. We propose that symbiotic interactions may influence the evolution of seed number and weight trade-off.     

Copy number variation and association over T-cell receptor genes—influence of DNA source

Genomic copy number variants (CNVs) are a common, heritable source of inter-individual differences in genomic sequence. Their influence on phenotypic variability and their involvement in the pathogenesis of several common diseases is well established and the object of many current studies. In the course of examining CNV association to various quantitative traits in a general population, we have detected a strong association of CNVs over the four TCR genes to lymphocyte and neutrophil numbers in blood. In a small replication series, we have further characterized the nature of these CNVs and found them not to be germline, but dependent on the origin of analysed DNA. Germline deletion and rearrangement around the T-cell receptor (TCR) genes naturally occurs in white blood cells. Blood DNA derived from persons with high lymphocyte counts generates variable intensity signals which behave like germline CNVs over these genes. As DNA containing a relative high proportion of these CNV-like events involving the TCR genes has the ability to influence genotype counts of SNPs in the regions of these genes, care should be taken in interpreting and replicating association signals on variants within these genes when blood-derived DNA is the only source of data.     

A texture-processing model of the ‘visual sense of number’

It has been suggested that numerosity is an elementary quality of perception, similar to colour. If so (and despite considerable investigation), its mechanism remains unknown. Here, we show that observers require on average a massive difference of approximately 40% to detect a change in the number of objects that vary irrelevantly in blur, contrast and spatial separation, and that some naive observers require even more than this. We suggest that relative numerosity is a type of texture discrimination and that a simple model computing the contrast energy at fine spatial scales in the image can perform at least as well as human observers. Like some human observers, this mechanism finds it harder to discriminate relative numerosity in two patterns with different degrees of blur, but it still outpaces the human. We propose energy discrimination as a benchmark model against which more complex models and new data can be tested.     

Super-resolution microscopy reveals the number and distribution of topoisomerase IIα and CENH3 molecules within barley metaphase chromosomes

Chromosoma - Topoisomerase IIα (Topo IIα) and the centromere-specific histone H3 variant CENH3 are key proteins involved in chromatin condensation and centromere determination,...     

Influence of odd and even number of Stone–Wales defects on the fracture behaviour of an armchair single-walled carbon nanotube under axial and torsional strain

Using Brenner's bond-order potential to represent the interaction of the in-plane C–C bond, an armchair (8,8) single-walled carbon nanotube is investigated by molecular dynamics simulation under axial loading and twist, both for perfect and imperfect lattices introducing an increasing number of Stone–Wales (SW) defects. The Young modulus, shear modulus, tensile strength, shear strength, ductility, stiffness and toughness are computed. All the mechanical characteristics are found to change appreciably by the inclusion of SW defects. Two distinct patterns of fracture mode are observed with odd and even numbers of defects. A clear evidence of the defect–defect interaction is observed when more than one defect is included.     

High-performance liquid chromatographic determination of phenol, 4-nitrophenol, β-naphthol and a number of their glucuronide and sulphate conjugates in organ perfusate

This paper describes a simple and more sensitive reversed-phase HPLC method for the quantification of phenol, 4-nitrophenol and β-naphthol and some of their glucuronide and sulphate conjugates in aqueous solution and liver perfusate buffer. Methanol-water mobile phases with ion-pairing agents for each phenolic group are detailed. The assay showed good recovery, accuracy and precision and is suitable for the quantification of these phenolic compounds in liver perfusion experiments.     

The base number of ��loxoscaphoid�� Asplenium species and its implication for cytoevolution in Aspleniaceae

Background and Aims

‘Loxoscaphoid’ Asplenium species are morphologically a remarkably distinct group of Aspleniaceae. Except for two preliminary chromosome counts of Asplenium theciferum, the cytology of this group of species has, however, been largely unstudied.

Methods

Chromosome counts were obtained by acetocarmine squash preparations of one mitotic cell and several meiotic cells. Relative DNA content of gametophytic and sporophytic cells was determined by flow cytometry. The phylogenetic placement of A. loxoscaphoides, A. rutifolium s.l. and A. theciferum s.l. was investigated through an analysis of rbcL sequences.

Key Results

The dysploid base number is reported to be x = 35 in Asplenium centrafricanum, A. loxoscaphoides, A. sertularioides and A. theciferum. Analysis of rbcL sequences confirms that ‘loxoscaphoids’ nest robustly within Asplenium. Several high ploidy levels exceeding the tetraploid level were found in A. theciferum s.l. and A. rutifolium s.l. All taxa proved to be sexual.

Conclusions

Four base numbers are known at present for Aspleniaceae: x = 39, 38, 36 and 35. The dysploid base number x = 35 found in the ‘loxoscaphoid’ Asplenium spp. sheds a novel light on the cytoevolution of the whole family. We postulate a recurrent descending dysploid evolution within Aspleniaceae, leading to speciation at the (sub)generic and species/group level.     

Identification and characterization of a QTL on chromosome 2 for cytosolic glutamine synthetase content and panicle number in rice

A quantitative trait locus (QTL) associated with the protein content of cytosolic glutamine synthetase (GS1; EC 6.3.1.2) in senescing leaves, panicle number, and panicle weight was characterized in rice (Oryza sativa L.). A near-isogenic line (NIL), C-22, developed by marker-assisted selection was grown under different nitrogen levels in the greenhouse and in a paddy field. Chromosome 2 of C-22 had an approximately 50-cM segment substituted from the Kasalath (indica) chromosome in a Koshihikari (japonica) genetic background. C-22 showed a 12–37% lower content of GS1 protein in leaf blades than Koshihikari, which was in good agreement with a QTL region positively affected by the japonica chromosome. At an early vegetative stage, C-22 had more active tillers than Koshihikari in the greenhouse. At the reproductive stage, both panicle number and total panicle weight of C-22 were significantly higher than those of Koshihikari, particularly when the plants were grown under a low-nitrogen condition. These traits of C-22 were further confirmed in a paddy field. Thus, tiller development was positively affected by the Kasalath chromosome at an early vegetative stage, which resulted in an increased panicle number and panicle weight at the mature stage in C-22. These data indicate that the target QTL (Pnn1; panicle number 1) is important in the development of tillers and panicles in rice. Linkage analyses for panicle number and ratio of developing tiller formation in the second axil (RDT) revealed that Pnn1 was delimited at the 6.7-cM region.     

Synthesis of archaeal glycolipid adjuvants-what is the optimum number of sugars?

As part of a programme to optimize the use of archaeal-lipid liposomes (archaeosomes) as vaccine adjuvants, we present the synthesis and immunological testing of an oligomeric series of mannose glycolipids (Manp(1-5)). To generate the parent archaeol alcohol precursor, the polar lipids extracted from the archaeon Halobacterium salinarum were hydrolyzed to remove polar head groups, and the archaeol so generated partitioned into diethyl ether. This alcohol was then iteratively glycosylated with the donor 2-O-acetyl-3,4,6-tri-O-benzyl-alpha/beta-d-mannopyranosyl trichloroacetimidate to yield alpha-Manp-(1-->2) oligomers. A starch-derived trimer was also synthesized as a control. To promote hydration and form stable archaeosomes, an archaeal anionic lipid archaetidylglycerol (AG) was included in a 4:1 molar ratio. Archaeosomes prepared from Manp(1-2)-AG were recovered at only 34-37%, whereas Manp(3-4)-AG recoveries were 72-77%. Lipid recovery following hydration of Manp(5)-AG archaeosomes declined to 34%, indicating an optimum of 3-4 Manp units for bilayer formation. The CD8(+) T cell response in mice immunized with Manp(3-5) archaeosomes containing ovalbumin was highest for Manp(4) and declined for Manp(3) and Manp(5), revealing an optimum length of four unbranched units. The starch-derived trimer was more active than the Manp oligomers, suggesting the involvement of either a general binding lectin on antigen-presenting cells with highest affinity for triglucose or multiple lectin receptors.     

Is there a fixed number of niches for endoparasites of fish?

Kennedy and Guégan, based on Cornell and Lawton (J Anim Ecol 1992;61:1–12), found a curvilinear relationship (the fundamental form of the relationship for parasite communities) between infracommunity and component community richness, and interpreted this as meaning that only processes acting within the infracommunities can explain the limitation in the number of parasite species in a given host. The research described here shows that an asymptotic relationship is the consequence of the differential likelihoods of parasite species to appear in an infracommunity as determined by transmission rates and intrinsic lifespans. Processes operating at the infracommunity level are not necessary to explain the curvilinear relationship. Even communities much richer than those found in European freshwater fishes cannot be assumed to be saturated in the sense that further species cannot be added over evolutionary time.     

Breeding status affects motoneuron number and muscle size in naked mole-rats: recruitment of perineal motoneurons?

Naked mole-rats live in large colonies and exhibit a strict reproductive hierarchy. Each colony has one breeding female and one to three breeding males; all other individuals are nonreproductive subordinates. Subordinates show a remarkable lack of sex differences in behavior and anatomy, but can become reproductive if removed from the colony. We recently reported that the striated perineal muscles and their innervating motoneurons, which are sexually dimorphic in all other mammals examined to date, are not dimorphic in subordinate naked mole-rats. Here we asked whether sexual differentiation of this neuromuscular system occurs when a subordinate becomes a breeder. The size and number of cells within Onuf's nucleus (homologue of the rat spinal nucleus of the bulbocavernosus) as well as perineal muscle volume were examined in subordinate and breeding naked mole-rats of both sexes. Sex differences in perineal motoneurons were not observed, regardless of social status. To our surprise, however, counts of motoneurons in Onuf's nucleus were increased approximately 30% in breeders of both sexes. This was accompanied by a reciprocal decrease in cells in Onuf's nucleus that were characterized by small soma size, and lacked a clear nucleus or nucleolus. Although not exhibiting typical motoneuron morphology, some of these small cells were positive for the motoneuron marker, SMI-32. The neuronal changes correlate with increased perineal muscle volumes in breeders. We propose that small, relatively undifferentiated cells are recruited to the pool of large Onuf's nucleus motoneurons when subordinate naked mole-rats become breeders.     

Measurement of the number of ornithine decarboxylase molecules in rat and mouse tissues under various physiological conditions by binding of radiolabelled α-difluoromethylornithine

The binding of alpha-difluoromethylornithine, an irreversible inhibitor, to ornithine decarboxylase was used to investigate the amount of enzyme present in rat liver under various conditions and in mouse kidney after treatment with androgens. Maximal binding of the drug occurred on incubation of the tissue extract for 60min with 3mum-difluoromethyl[5-(14)C]ornithine in the presence of pyridoxal phosphate. Under these conditions, only one protein became labelled, and this corresponded to ornithine decarboxylase, having M(r) about 100000 and subunit M(r) about 55000. Treatment of rats with thioacetamide or carbon tetrachloride or by partial hepatectomy produced substantial increases in ornithine decarboxylase activity and parallel increases in the amount of enzyme protein as determined by the extent of binding of difluoromethyl[5-(14)C]ornithine. Similarly, treatment with cycloheximide or 1,3-diaminopropane greatly decreased both the enzyme activity and the amount of difluoromethyl-[5-(14)C]ornithine bound to protein. In all cases, the ratio of drug bound to activity was 26fmol/unit, where 1 unit corresponds to 1nmol of substrate decarboxylated in 30min. These results indicate that even after maximal induction of the enzyme in rat liver there is only about 1ng of enzyme present per mg of protein. When mice were treated with androgens there was a substantial increase in renal ornithine decarboxylase activity, the magnitude of which depended on the strain. There was an excellent correspondence between the amount of activity present and the capacity to bind labelled alpha-difluoromethylornithine in the mouse kidney extracts, but in this case the ratio of drug bound to activity was 14fmol/unit, suggesting that the mouse enzyme has a higher catalytic-centre activity. After androgen induction, the mouse kidney extracts contain about 170ng of enzyme/mg of protein. These results indicate that titration with alpha-difluoromethylornithine provides a valuable method by which to quantify the amount of active ornithine decarboxylase present in mammalian tissues, and that the androgen-treated mouse kidney is a much better source for purification of the enzyme than is rat liver.