Unequal Abundance Research Articles

Diversidad y patrón de emergencia de libélulas en un hábitat léntico del Jardín Botánico Nacional de Cuba

The transference of biomass to terrestrial ecosystems is carried out in part by the adults of aquatic insects after their emergence from water, as it is in the case of odonates. The aim of this study is to characterize the emergence pattern of an odonate assemblage in an artificial lentic habitat of the National Botanical Garden of Cuba, from the harvest of exuviae. Fifty two samplings were carried out with a frequency of once a week, and an interval of seven to nine days, in four transect of 8 m2. To characterize the emergence, the seasonal climate model was considered: rainy, poorly rainy and transition seasons. The change in climatic variables and habitat characteristics was registered, and was related to the emergence pattern. The variation in the use of resources during emergence was described. The emergence with a constant volume of water turned out to be asynchronous, with a predominance of accidental species and unequal abundance distribution. The rainy period was the season with the highest percentage of emergence, in which rainfall and relative humidity were the factors that most influenced the emergence pattern. The plants were the most used emergence substrate, and the decrease in vegetation cover corresponded to the alternative use of other substrates. Citation: Lim, G. & Trapero-Quintana, A. 2020. Diversidad y patron de emergencia de libelulas en un habitat lentico del Jardin Botanico Nacional de Cuba. Revista Jard. Bot. Nac. Univ. Habana 41: 119-130. Article history: Received: 17 February 2020. Accepted: 15 June 2020. Online: 4 November 2020. Editor: Luis Manuel Leyva

Genetic variability, chemotype distribution, and aggressiveness of Fusarium culmorum on durum wheat in Tunisia

Fusarium culmorum is the most commonly reported root rot pathogen in Tunisian durum wheat. Isolates of the pathogen from four durum wheat growing areas in the north of Tunisia were analyzed for their chemotypes. Two chemotypes were detected at unequal abundance (96% of 3-ADON and 4% of NIV). Distribution of a SNP mutation located at the position 34 bp after the first exon of the EF-1α partial sequence was analysed, to verify whether the haplotype was specifically associated to Fusarium root rot. A and T haplotypes were homogeneously distributed in three different Tunisian regions (Mateur, Beja and Bousalem) but not for the region of Bizerte, from which greatest number of A haplotype strains were detected. The isolates were tested for their virulence under glasshouse conditions, and a mean of 91% of crown and root infection was observed. Chemotype influenced virulence, but there was no significant influence of the geographical origin or haplotype on virulence. The distribution of three inter simple sequence repeats (ISSR) was examined, to better understand the structure of F. culmorum populations in Tunisia. A total of 27 fragments were obtained with eight polymorphic bands. Cluster analysis showed a high level of similarity between isolates. Analysis of molecular variance confirmed that there was little genetic differentiation among F. culmorum strains from different locations.

Analysis of the Quaternary Structure of Hemoglobin Beckman Variant and Molecular Interpretation of Its Functional Abnormality: A Mass-Spectrometry-Based Approach.

Electrostatic attraction between α and β globin chains holds the subunits together in a tetrameric human hemoglobin molecule (α2 β2 ). Compared to normal globin chains, the affinity of a mutant chain to its partner globin might be different in genetic variants of hemoglobin. This leads to an unequal abundance of normal and variant hemoglobin in heterozygous samples, even though the rates of synthesis of both the normal and variant chains are the same. The aforementioned affinities across various globin chains might be assessed by quantification of the different forms of the tetramers present in a variant hemoglobin sample. In the present study, by exploiting mass differences between globin chains, differently populated hemoglobin tetramers present in hemoglobin (Hb) Beckman, a β variant (βA135D), were structurally characterized. The relative populations of dissymmetric tetramers (α2 β2 , α2 ββV , and α2 βV2 ) indicated that both β and βV have different affinities towards the α globin chain. Conformational dynamics analyzed from hydrogen/deuterium exchange kinetics of the three peptide fragments of Hb Beckman in its oxy state displayed molecular insight into its functional abnormality. However, in comparison to normal hemoglobin (α2 β2 ), the point mutation did not show any change in the collision cross-sections of the functionally active conformers of the variant hemoglobin molecules (α2 ββV and α2 βV2 ).

Genome-wide analysis of brain and gonad transcripts reveals changes of key sex reversal-related genes expression and signaling pathways in three stages of Monopterus albus.

BackgroundThe natural sex reversal severely affects the sex ratio and thus decreases the productivity of the rice field eel (Monopterus albus). How to understand and manipulate this process is one of the major issues for the rice field eel stocking. So far the genomics and transcriptomics data available for this species are still scarce. Here we provide a comprehensive study of transcriptomes of brain and gonad tissue in three sex stages (female, intersex and male) from the rice field eel to investigate changes in transcriptional level during the sex reversal process.ResultsApproximately 195 thousand unigenes were generated and over 44.4 thousand were functionally annotated. Comparative study between stages provided multiple differentially expressed genes in brain and gonad tissue. Overall 4668 genes were found to be of unequal abundance between gonad tissues, far more than that of the brain tissues (59 genes). These genes were enriched in several different signaling pathways. A number of 231 genes were found with different levels in gonad in each stage, with several reproduction-related genes included. A total of 19 candidate genes that could be most related to sex reversal were screened out, part of these genes’ expression patterns were validated by RT-qPCR. The expression of spef2, maats1, spag6 and dmc1 were abundant in testis, but was barely detected in females, while the 17β-hsd12, zpsbp3, gal3 and foxn5 were only expressed in ovary.ConclusionThis study investigated the complexity of brain and gonad transcriptomes in three sex stages of the rice field eel. Integrated analysis of different gene expression and changes in signaling pathways, such as PI3K-Akt pathway, provided crucial data for further study of sex transformation mechanisms.

Whole Mitochondrial Genome Sequencing and Re-Examination of a Cytoplasmic Male Sterility-Associated Gene in Boro-Taichung-Type Cytoplasmic Male Sterile Rice.

Nuclear genome substitutions between subspecies can lead to cytoplasmic male sterility (CMS) through incompatibility between nuclear and mitochondrial genomes. Boro-Taichung (BT)-type CMS rice was obtained by substituting the nuclear genome of Oryza sativa subsp. indica cultivar Chinsurah Boro II with that of Oryza sativa subsp. japonica cultivar Taichung 65. In BT-type CMS rice, the mitochondrial gene orf79 is associated with male sterility. A complete sequence of the Boro-type mitochondrial genome responsible for BT-type CMS has not been determined to date. Here, we used pyrosequencing to construct the Boro-type mitochondrial genome. The contiguous sequences were assembled into five circular DNA molecules, four of which could be connected into a single circle. The two resulting subgenomic circles were unable to form a reliable master circle, as recombination between them was scarcely detected. We also found an unequal abundance of DNA molecules for the two loci of atp6. These results indicate the presence of multi-partite DNA molecules in the Boro-type mitochondrial genome. Expression patterns were investigated for Boro-type mitochondria-specific orfs, which were not found in the mitochondria from the standard japonica cultivar Nipponbare. Restorer of fertility 1 (RF1)-dependent RNA processing has been observed in orf79-containing RNA but was not detected in other Boro-type mitochondria-specific orfs, supporting the conclusion that orf79 is a unique CMS-associated gene in Boro-type mitochondria.

Unequal allelic expression of wild-type and mutated β-myosin in familial hypertrophic cardiomyopathy.

Familial hypertrophic cardiomyopathy (FHC) is an autosomal dominant disease, which in about 30% of the patients is caused by missense mutations in one allele of the β-myosin heavy chain (β-MHC) gene (MYH7). To address potential molecular mechanisms underlying the family-specific prognosis, we determined the relative expression of mutant versus wild-type MYH7-mRNA. We found a hitherto unknown mutation-dependent unequal expression of mutant to wild-type MYH7-mRNA, which is paralleled by similar unequal expression of β-MHC at the protein level. Relative abundance of mutated versus wild-type MYH7-mRNA was determined by a specific restriction digest approach and by real-time PCR (RT-qPCR). Fourteen samples from M. soleus and myocardium of 12 genotyped and clinically well-characterized FHC patients were analyzed. The fraction of mutated MYH7-mRNA in five patients with mutation R723G averaged to 66 and 68% of total MYH7-mRNA in soleus and myocardium, respectively. For mutations I736T, R719W and V606M, fractions of mutated MYH7-mRNA in M. soleus were 39, 57 and 29%, respectively. For all mutations, unequal abundance was similar at the protein level. Importantly, fractions of mutated transcripts were comparable among siblings, in younger relatives and unrelated carriers of the same mutation. Hence, the extent of unequal expression of mutated versus wild-type transcript and protein is characteristic for each mutation, implying cis-acting regulatory mechanisms. Bioinformatics suggest mRNA stability or splicing effectors to be affected by certain mutations. Intriguingly, we observed a correlation between disease expression and fraction of mutated mRNA and protein. This strongly suggests that mutation-specific allelic imbalance represents a new pathogenic factor for FHC.Electronic supplementary materialThe online version of this article (doi:10.1007/s00395-011-0205-9) contains supplementary material, which is available to authorized users.

Life history traits predict relative abundance in an assemblage of forest caterpillars

Species in a given trophic level occur in vastly unequal abundance, a pattern commonly documented but poorly explained for most taxa. Theoretical predictions of species density such as those arising from the metabolic theory of ecology hold well at large spatial and temporal scales but are not supported in many communities sampled at a relatively small scale. At these scales ecological factors may be more important than the inherent limits to energy use set by allometric scaling of mass. These factors include the amount of resources available, and the ability of individuals to convert these resources successfully into population growth. While previous studies have demonstrated the limits of macroecological theory in explaining local abundance, few studies have tested alternative generalized mechanisms determining abundance at the community scale. Using an assemblage of forest moth species found co-occurring as caterpillars on a single host plant species, we tested whether species abundance on that plant could be explained by mass allometry, intrinsic population growth, diet breadth, or some combination of these traits. We parameterized life history traits of the caterpillars in association with the host plant in both field and laboratory settings, so that the population growth estimate was specific to the plant on which abundance was measured. Using a generalized least-squares regression method incorporating phylogenetic relatedness, we found no relationship between abundance and mass but found that abundance was best explained by both intrinsic population growth rate and diet breadth. Species population growth potential was most affected by survivorship and larval development time on the host plant. Metabolic constraints may determine upper limits to local abundance levels for species, but local community abundance is strongly predicted by the potential for population increase and the resources available to that species in the environment.

Life history traits predict relative abundance in an assemblage of forest caterpillars

Species in a given trophic level occur in vastly unequal abundance, a pattern commonly documented but poorly explained for most taxa. Theoretical predictions of species density such as those arising from the metabolic theory of ecology hold well at large spatial and temporal scales but are not supported in many communities sampled at a relatively small scale. At these scales ecological factors may be more important than the inherent limits to energy use set by allometric scaling of mass. These factors include the amount of resources available, and the ability of individuals to convert these resources successfully into population growth. While previous studies have demonstrated the limits of macroecological theory in explaining local abundance, few studies have tested alternative generalized mechanisms determining abundance at the community scale. Using an assemblage of forest moth species found co-occurring as caterpillars on a single host plant species, we tested whether species abundance on that plant could be explained by mass allometry, intrinsic population growth, diet breadth, or some combination of these traits. We parameterized life history traits of the caterpillars in association with the host plant in both field and laboratory settings, so that the population growth estimate was specific to the plant on which abundance was measured. Using a generalized least-squares regression method incorporating phylogenetic relatedness, we found no relationship between abundance and mass but found that abundance was best explained by both intrinsic population growth rate and diet breadth. Species population growth potential was most affected by survivorship and larval development time on the host plant. Metabolic constraints may determine upper limits to local abundance levels for species, but local community abundance is strongly predicted by the potential for population increase and the resources available to that species in the environment.

Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification

Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but low microbial biomass often prevents application of this technology to many natural microbial communities. We developed a whole-community genome amplification-assisted microarray detection approach based on multiple displacement amplification. The representativeness of amplification was evaluated using several types of microarrays and quantitative indexes. Representative detection of individual genes or genomes was obtained with 1 to 100 ng DNA from individual or mixed genomes, in equal or unequal abundance, and with 1 to 500 ng community DNAs from groundwater. Lower concentrations of DNA (as low as 10 fg) could be detected, but the lower template concentrations affected the representativeness of amplification. Robust quantitative detection was also observed by significant linear relationships between signal intensities and initial DNA concentrations ranging from (i) 0.04 to 125 ng (r2 = 0.65 to 0.99) for DNA from pure cultures as detected by whole-genome open reading frame arrays, (ii) 0.1 to 1,000 ng (r2 = 0.91) for genomic DNA using community genome arrays, and (iii) 0.01 to 250 ng (r2 = 0.96 to 0.98) for community DNAs from ethanol-amended groundwater using 50-mer functional gene arrays. This method allowed us to investigate the oligotrophic microbial communities in groundwater contaminated with uranium and other metals. The results indicated that microorganisms containing genes involved in contaminant degradation and immobilization are present in these communities, that their spatial distribution is heterogeneous, and that microbial diversity is greatly reduced in the highly contaminated environment.

Abundance and life cycle of Zonocerus variegatus (Orthoptera: Pyrgomorphidae) in the humid forest zone of southern Cameroon

AbstractWeekly captures from January 2000 to January 2002 enabled us to study the abundance and life cycle of the variegated grasshopper, Zonocerus variegatus (Orthoptera: Pyrgomorphidae), in the humid forest zone of Southern Cameroon. We found that Z. variegatus was present throughout the year in the forest reserve and the human‐influenced zones of Yaounde and Mbalmayo in two univoltine populations, which had unequal abundance and durations. The separation of the two populations was clearer in the Yaounde and Mbalmayo developed zones than in the Mbalmayo forest reserve (undeveloped zone). The abundance of Z. variegatus varied according to the post‐embryonic stage, sex, year and season. Hatching and coupling took place during the dry and rainy seasons, whereas oviposition occurred only in the rainy season. In Cameroon, the type of life cycle of Z. variegatus observed in the humid forest zone of the south is different from that of the “Sudanian and Sahelian” zones.

Solitary human endogenous retroviruses-K LTRs retain transcriptional activity in vivo, the mode of which is different in different cell types.

Solitary long terminal repeats (LTRs) of human endogenous retroviruses (HERVs), tens of thousands of which are spread all over the genome, contain a variety of potential transcription regulatory elements. Information on transcriptional behavior of individual solitary LTRs, however, is limited. We studied the transcriptional activity of several individual HERV-K LTRs in a variety of tissues and cell lines. The RT-PCR technique targeted at specific amplification of the U3 or U5 regions of individual LTRs together with their unique genomic flanks was used to estimate the content of each region in the transcripts. An unequal abundance of the U3 and U5 regions of the transcripts of the same LTR in different cells and tumors was observed. Each LTR is transcribed differently in different cells or tissues, and transcriptional behavior of different LTRs was different in the same cell line or tissue. The transcriptional status of LTRs varies in response to mitogenic and stress factors and in tumor tissues compared to normal counterparts. The LTRs thus seem to be the subjects of specific transcription regulation. The data obtained indicate that an appreciable fraction of the LTRs retained regulatory potential throughout millions of years of evolution and thus may contribute to the overall transcription regulatory network.

Evaluating Dispersal Estimates Using mtDNA Data: Comparing Analytical and Simulation Approaches

Abstract: Using genetic data to estimate dispersal is attractive because direct estimation is often infeasible. Unfortunately, analytical tools remain rudimentary. Various standard population genetic formulae estimate dispersal rates between populations but require unrealistic assumptions, such as equal population size. Recent increases in computer speed enable simulations of genetic processes in populations. We designed simulation models to evaluate the adequacy of using analytical formulae to estimate dispersal rates needed for conservation decisions. Our models incorporated genetic stochasticity. They adhered closely to the assumptions of the standard formulae except that we relaxed the assumption that all populations were equal in size. We found that measures of population differentiation, such as the statistic ΦS T , varied greatly over time, reflecting the stochastic nature of genetic systems. In some cases, however, even large amounts of variation over time made no difference in defining population structure for management purposes, whereas in other cases the opposite was true. Statistics of genetic differentiation were so variable that management decisions based on analytical formulae would often be incorrect. Adjoining populations with little dispersal between them that should be managed separately were by chance alone so genetically similar that they appear panmictic, incorrectly implying that they should be managed as a single unit. The form of distributions of these statistics was complex and did not conform to standard statistical distributions. Furthermore, differences between these distributions for equal and unequal abundance cases indicated that pursuits of simple adjustments to analytical formulae are unlikely to be fruitful. In contrast, our simulation technique can be used in a decision analysis framework because it incorporates uncertainties into a probability distribution. We conclude with a case in which a manager wants to know whether current human‐caused mortality levels can be sustained while maintaining the local population at healthy levels. The example demonstrates how decision analysis for population structure can use the probability distributions generated from simulations to incorporate uncertainty and estimate over‐ and underprotection errors.

Minilibraries constructed from cDNA generated by arbitrarily primed RT-PCR: an alternative to normalized libraries for the generation of ESTs from nanogram quantities of mRNA

The generation of expressed sequenced tags (ESTs) depends on the arbitrary selection of individual cDNA clones from libraries. The efficiency of this process reflects the clonal structure of the library used and can be significantly increased using size selected, directional, normalized cDNA libraries. This strategy, however, is not readily applicable when mRNA is limiting, as is the case in the study of complex microorganisms such as parasites, fetal tissues or tumor biopsies. We show here that the construction and systematic sequencing of minilibraries of cDNAs produced by arbitrarily primed PCR provides an alternative means of efficiently generating ESTs in situations where only nanogram quantities of RNA are available. This methodology greatly compensates for unequal message abundance, avoids the need for complex library construction, is equally applicable to the analysis of abundant or rare biological material and is ideally suited to multicenter programmes.

Urinary excretion of the enantiomers of 1-methyl-1,2,3,4-tetrahydro-beta-carboline in unequal abundance implies enzymatic metabolism in man.

1-Methyl-1,2,3,4-tetrahydro-beta-carboline, a condensation product of tryptamine and acetaldehyde, is one of the neuropharmacologically active alkaloids in mammals. Its enantiomers excreted in human urine were independently analyzed by gas chromatography-negative ion chemical ionization mass spectrometry. Mass fragmentograms of the racemic 1-methyl-1,2,3,4-tetrahydro-beta-carboline offered two peaks with (S)-(-)- and (R)-(+)-configurations which were eluted in this retention order. When the racemic tetradeuterated 1-methyl-1,2,3,4-tetrahydro-beta-carboline was orally administered to a human subject, the urinary tetradeuterated enantiomers were found to be of unequal abundance. The deuterated (R)-(+)-1-methyl-1,2,3,4-tetrahydro-beta-carboline was predominantly excreted in human urine about 3-times over the deuterated (S)-(-)-one. The stereoselective difference in the urinary excretion of 1-methyl-1,2,3,4-tetrahydro-beta-carboline administered exogenously implies that it is enzymatically metabolized, but not that its biosynthesis is associated with an enzymatic reaction.

In vitro study of the aromatic hydroxylation of 1-methyltetrahydro-β-carboline (methtryptoline) in rat

The incubation of 1-methyltetrahydro-β-carboline (1-MeTHBC) with hepatocytes isolated from 3-methylcholanthrene-treated rats led to formation of the 5-, 6- and 7-hydroxylated products. The hydroxylating activity was associated with the microsomal fraction as indicated by testing different subcellular fractions. The highest activity for hydroxylating 1-MeTHBC was found in liver which was about ten times as active as lung. Only a trace amount of hydroxylating activity was present in brain and kidney tissue. Analysis using chiral gas chromatography revealed an unequal abundance of enantiomers in all three products. The formation of the 5-, 6- and 7-hydroxylated products was confirmed in vivo by analysis of 24 h urine samples after intraperitoneal administration of 1-MeTHBC to 3-methylcholanthrene-treated rats.

Significance of developmental stages in the coexistence of three species of Mononchoidea (Nematoda) in a pasture soil

Populations of each developmental stage of three mononchid species (Clarkus, Cobbonchus, Iotonchus) under grazed pasture were estimated in the presence and absence of the earthworm Aporrectodea caliginosa. All stages of all species had signs of prey in their gut. Introduction of earthworms changed the abundance of the species from 158000, 84000 and 2400/m2 to 43 000, 5000 and 41300/m2, but total biomass remained relatively unchanged at 288000 μg/m2. The larger Iotonchus was more abundant in the soil with earthworms and improved texture. The length ratios between the stages of the three species are 1.225, 1.235 and 1.395, with the overall mean of 1.285 close to the value for the Dyar-Hutchinson rule. Other analyses of population separation are made. Given the unequal abundance of the various stages, the species successfully coexist and exploit a wide resource. Predation by such nematodes on bacterial-feeding nematodes may influence bacterial grazing and thus nutrient cycling.

The solution constitution of the roussin ester Fe2(SBu-t)2(NO)4

The1H and15N NMR spectra of the Roussin ester Fe2(SBu-t)2(NO)4 show that in solution it exists as a mixture of two isomeric forms (I andII), of C2h- and C2v- symmetry, respectively. Unlike other similar esters, Fe2(SR)2(NO)4, the isomers are present in non-equal proportions: the equilibrium constant K = [II]/[I] is unchanged in the temperature range 220–298 K, indicating that entropy factors are primarily responsible for the unequal abundance ofI andII.

Tau as an index of similarity in community comparisons: an approach permitting the hypothesis of unequal species abundance

P. A. Jumars (Ecology, 61: 1553–1554. 1980) has argued that in significance tests of τ where it is employed in community comparisons, the null hypothesis that all rankings of species are equally likely can be translated only into the hypothesis that all species are equally abundant. An alternative translation is presented, in which it is the species names that are equally likely to be attached to unequal partitionings of the population. Some biological justifications for this alternative model are offered. It is shown that Jumars' example calculations illustrate type II rather than type I statistical errors, so that the "serious doubt" that he expresses about published community comparison significance tests applies to acceptances rather than rejections of the null. The alternative index of community similarity he proposes, based upon contingency table analyses of species counts, is shown to reflect excessive sampling homogeneity rather than community similarity.

The Limiting Similarity, Convergence, and Divergence of Coexisting Species

1. There is a limit to the similarity (and hence to the number) of competing species which can coexist. The total number of species is proportional to the total range of the environment divided by the niche breadth of the species. The number is reduced by unequal abundance of resources but increased by adding to the dimensionality of the niche. Niche breadth is increased with increased environmental uncertainty and with decreased productivity. 2. There is a different evolutionary limit, L, to the similarity of two coexisting species such that a) If two species are more similar than L, a third intermediate species will converge toward the nearer of the pair. b) If two species are more different than L, a third intermediate species will diverge from either toward a phenotype intermediate between the two.