Using lod scores to detect sex differences in male-female recombination fractions

Human recombination fraction (RF) can differ between males and females, but investigators do not always know which disease genes are located in genomic areas of large RF sex differences. Knowledge of RF sex differences contributes to our understanding of basic biology and can increase the power of a linkage study, improve gene localization, and provide clues to possible imprinting. One way to detect these differences is to use lod scores. In this study we focused on detecting RF sex differences and answered the following questions, in both phase-known and phase-unknown matings: (1) How large a sample size is needed to detect a RF sex difference? (2) What are "optimal" proportions of paternally vs. maternally informative matings? (3) Does ascertaining nonoptimal proportions of paternally or maternally informative matings lead to ascertainment bias? Our results were as follows: (1) We calculated expected lod scores (ELODs) under two different conditions: "unconstrained," allowing sex-specific RF parameters (theta(female), theta(male)); and "constrained," requiring theta(female) = theta(male). We then examined the DeltaELOD (identical with difference between maximized constrained and unconstrained ELODs) and calculated minimum sample sizes required to achieve statistically significant DeltaELODs. For large RF sex differences, samples as small as 10 to 20 fully informative matings can achieve statistical significance. We give general sample size guidelines for detecting RF differences in informative phase-known and phase-unknown matings. (2) We defined p as the proportion of paternally informative matings in the dataset; and the optimal proportion p(circ) as that value of p that maximizes DeltaELOD. We determined that, surprisingly, p(circ) does not necessarily equal (1/2), although it does fall between approximately 0.4 and 0.6 in most situations. (3) We showed that if p in a sample deviates from its optimal value, no bias is introduced (asymptotically) to the maximum likelihood estimates of theta(female) and theta(male), even though ELOD is reduced (see point 2). This fact is important because often investigators cannot control the proportions of paternally and maternally informative families. In conclusion, it is possible to reliably detect sex differences in recombination fraction.     

Patterns of sexual dimorphism in the Persian Leopard (Panthera pardus saxicolor) and implications for sex differentiation

Extant felids show a high degree of inter-sexual dimorphism, meaning significant size differences between males and females. Such a differentiation may have various ecological, behavioural and evolutionary implications, at both species and subspecies levels. We have investigated the sexual size differences in one of the most dimorphic felids, i.e. the Leopard (Panthera pardus), based on 63 craniometric and 55 morphometric samples from Iran which belong to the subspecies Persian Leopard (P. p. saxicolor). In order to explore patterns of sexual dimorphism, multivariate statistical analysis on 24 skull variables as well as univariate approaches for two body measurements were applied. We found significant inter-sexual differences in skull size whereas it was not meaningful after removing the effect of size to address skull shape. Moreover, inter-sexual differentiation was also remarkable when comparing morphometric body measurements in adults, showing that the males possess a larger head mass and longer body, but sub-adults did not show any remarkable differentiation between sexes. A combination of craniometric and morphological features is proposed for sex differentiation in Leopards.     

Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model

Due to genetic variation in the ancestor of two populations or two species, the divergence time for DNA sequences from two populations is variable along the genome. Within genomic segments all bases will share the same divergence-because they share a most recent common ancestor-when no recombination event has occurred to split them apart. The size of these segments of constant divergence depends on the recombination rate, but also on the speciation time, the effective population size of the ancestral population, as well as demographic effects and selection. Thus, inference of these parameters may be possible if we can decode the divergence times along a genomic alignment. Here, we present a new hidden Markov model that infers the changing divergence (coalescence) times along the genome alignment using a coalescent framework, in order to estimate the speciation time, the recombination rate, and the ancestral effective population size. The model is efficient enough to allow inference on whole-genome data sets. We first investigate the power and consistency of the model with coalescent simulations and then apply it to the whole-genome sequences of the two orangutan sub-species, Bornean (P. p. pygmaeus) and Sumatran (P. p. abelii) orangutans from the Orangutan Genome Project. We estimate the speciation time between the two sub-species to be thousand years ago and the effective population size of the ancestral orangutan species to be , consistent with recent results based on smaller data sets. We also report a negative correlation between chromosome size and ancestral effective population size, which we interpret as a signature of recombination increasing the efficacy of selection.     

The human receptor for T-cell growth factor. Evidence for variable post-translational processing, phosphorylation, sulfation, and the ability of precursor forms of the receptor to bind T-cell growth factor

The T-cell growth factor (TCGF) receptor on phytohemagglutinin-activated normal peripheral blood T-cells is characterized as a glycoprotein with an apparent Mr = 55,000 that contains N-linked and O-linked carbohydrate with only approximately 33,000 daltons of peptide structure (p33) as evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. There are two N-linked glycosylated intermediate precursor forms (apparent Mr = 35,000 (p35) and 37,000 (p37]. This receptor differs from the TCGF receptor on HUT-102B2 cells (apparent Mr = 50,000) because of differences in post-translational processing. Experiments with the carboxylic ionophore monensin demonstrate blockade of the transition of the p35 and p37 receptor precursor forms to the mature receptor, presumably secondary to inhibition of Golgi-associated receptor processing. We identify the primary translation product of TCGF receptor mRNA as intermediate in size between the p33 and the p35/p37 forms. We further demonstrate that the p33, p35, and p37 precursor forms, but not the primary translation product, are all capable of binding TCGF. Thus, the removal of the signal peptide and/or conformational changes of the primary translation product are necessary for ligand binding; however, the extensive post-translational modifications are not. Lastly, we demonstrate that at least some TCGF receptors are phosphorylated and sulfated, and that TCGF receptors on phytohemagglutinin-activated normal T-cells are more heavily sulfated than those on HUT-102B2 cells.     

Variation in the 16S-23S rRNA intergenic spacer regions in Vibrio parahaemolyticus strains are due to indels nearby their tRNAGlu

Vibrio parahaemolyticus contains 11 rRNA operons each including one of six 16S-23S rRNA gene intergenic spacer classes differing in size and nucleotide sequence. Some of the spacer classes may differ between isolates. We observed that the differences in the spacers between isolates are generally in two spacer classes present in single copies in the genome, one class containing tRNA(Ala) and tRNA(Glu) and the other tRNA(Glu) exclusively. Moreover, these differences are due to indels located nearby their tRNA(Glu). Comparison of the nucleotide sequence between spacer classes suggests that intragenomic nonreciprocal recombination causes the size variations observed in the spacer regions of V. parahaemolyticus strains.     

Morphometric data on the lymph capillaries of the ventricles of the rabbit heart

A morphometric analysis was done on the lymph capillaries of both left and right ventricles from the rabbit heart. The measurements were made on the lymphatics identified in the subepicardium, myocardium and subendocardium of the ventricular walls. Quantitative evaluations were carried out on light and electron microscopic sections by a computerized image analysis system. The following parameters were selected and measured: (1) the diameter (of area-equivalent circle) of lymph capillaries, (2) the diameter of the uncoated micropinocytotic vesicles (located on the abluminal and adluminal side and in the cytoplasm of the endothelial cell) and the area occupied by the vesicles per unit area of cytoplasm. Differences in the size of the lymph capillaries were found in the three layers (subepicardium, myocardium and subendocardium) of the ventricular walls. The largest vessels were present in the subepicardium both in the left ventricle and in the right one. No significant variations were found in the lymphatics of corresponding regions on both ventricles. Little variations on the mean diameter of the uncoated micropinocytotic vesicles are present in the three regions of the endothelial wall. In the left ventricle only, the subendocardial vesicles are significantly larger than the subepicardial and the myocardial ones (p less than 0.05). The areal density occupied by vesicular system in the three layers of the ventricular wall showed significant differences in both ventricles (p less than 0.05). The vesicles present in the subepicardial vessels occupied the smallest areal density. No significant variations existed in the vesicular areal density between the two ventricles.(ABSTRACT TRUNCATED AT 250 WORDS)     

Wing size and shape variation of Phlebotomus papatasi (Diptera: Psychodidae) populations from the south and north slopes of the Atlas Mountains in Morocco

The wing shape and size morphology of populations of the medically important phlebotomine sand fly, Phlebotomus papatasi, were examined in two endemic (south of the Atlas Mountains) and nonendemic (north of the Atlas Mountains) foci of cutaneous leishmaniasis by using geometric morphometrics in Morocco. Although it is present in all of Morocco, P. papatasi is the main vector of Leishmania major in only southern part of the Atlas Mountains. There are four major mountain ranges that serve as geographical barriers for species distribution in the study area and at least four gaps were recognized among these barriers. We found statistically significant differences in wing shape morphology between southern and northern populations. Analysis clearly recognized two main groups of populations on both sides of the mountains. The graphical depiction of Principal Component Analysis (PCA) and Canonical Variates Analysis (CVA) confirmed our morphometric study suggesting that the difference in wing morphology between the populations indicates that the population of P. papatasi shows phenotypic plasticity in the study area. According to centroid size analyses, which were used as measures of wing size differences among different sites, the north population of P. papatasi had relatively larger wings than the south population.     

Size and fecundity in the Jamaican gall-midge Asphondylia boerhaaviae

ABSTRACT. 1. The gall-midge Asphondylia boerhaaviae Möhn galls weeds belonging to the Nyctaginaceae in Jamaica and other parts of the Caribbean. The species breeds throughout the year with a generation length of < 1 month.
2. In adult females, plots of wing length on hind tibial length, of maximum potential fecundity (m.p.f.) on wing length, and of m.p.f. on ovariole number, suggested the presence of a small morph, which the use of discriminant function analysis and other investigations confirmed. There was also good evidence of two size morphs in adult males.
3. Both body size and ovariole number had significant effects on m.p.f. but these effects were different in the two morphs. While the food plants had significant influences on size and fecundity, these were relatively small. The m.p.f. of the small morph was 125.8±11.1 eggs, and of the large morph 318.7±8.3 (95% cl).
4. Laboratory experiments on the flight performance of newly-emerged midges indicated that the small morph was not dispersive and that about 80% of the large morph was dispersive. No differences in size, wing length or fecundity could be found between the two behavioural types of the large morph.
5. The nature of the polymorphism is unusual, particularly since the dispersive individuals potentially have similar (or greater) fecundity than the non-dispersive ones.
6. Estimates of achieved fecundity (eggs actually laid, rather than m.p.f.) were 67.8±9.6 (field, minimum) and 138.9±30.4 (laboratory), the latter estimate being based on large-morph females.     

Morphometrics of the callitrichid forelimb: A case study in size and shape

Mosimann and colleagues formulated a technique that distinguishes between size and shape, based on the concept of geometric similarity and the distinction between log size-and-shape and log shape variables. We extend these formulations in an examination of the forelimb of three callitrichid species (adultSaguinus oedipus, Saguinus fuscicollis, andCallithrix jacchus). We employ principal components analysis to explore the relationship between variance explained by size-and-shape versus shape alone. Independence of shape vectors is examined via correlation analysis. Then we use log shape data to construct intersample (species means) and total sample (between all paris of individuals) matrices of average taxonomic distances. These distance matrices are subjected to cluster analysis and principal coordinate ordinations. Results of principal components analysis suggest that after isometric size is removed, there remains sufficient shape information to discriminate among the three taxa. Careful examination and quantification of the relationships between shape and size suggest that size information (e.g., geometric mean) is fundamental for understanding shape differences within and among callitrichid species; in other words, most aspects of forelimb shape are significantly correlated with size. Contrary to conventional wisdom, we also demonstrate that such correlations are not spurious. Ordinations and clustering of log shape distance matrices (based on means and individuals) support the notion that, despite differences in size, the two tamarins are more similar in shape than either is toC. jacchus (despite size similarity betweenS. fuscicollis andC. jacchus). Although shape variation in the forelimb of calliirichids may have a functional component, the phylogenetic signal remains strong and serves to group individuals accordingly.     

Differences in basal airway antioxidant concentrations are not predictive of individual responsiveness to ozone: a comparison of healthy and mild asthmatic subjects

The air pollutant ozone induces both airway inflammation and restrictions in lung function. These responses have been proposed to arise as a consequence of the oxidizing nature of ozone, depleting endogenous antioxidant defenses with ensuing tissue injury. In this study we examined the impact of an environmentally relevant ozone challenge on the antioxidant defenses present at the surface of the lung in two groups known to have profound differences in their antioxidant defense network: healthy control (HC) and mild asthmatic (MA) subjects. We hypothesized that baseline differences in antioxidant concentrations within the respiratory tract lining fluid (RTLF), as well as induced responses, would predict the magnitude of individual responsiveness. We observed a significant loss of ascorbate (ASC) from proximal (-45.1%, p <.01) and distal RTLFs (-11.7%, p <.05) in healthy subjects 6 h after the end of the ozone challenge. This was associated (Rs, -0.71, p <.01) with increased glutathione disulphide (GSSG) in these compartments (p =.01 and p <.05). Corresponding responses were not seen in asthmatics, where basal ASC concentrations were significantly lower (p <.01) and associated with elevated concentrations of GSSG (p <.05). In neither group was any evidence of lipid oxidation seen following ozone. Despite differences in antioxidant levels and response, the magnitude of ozone-induced neutrophilia (+20.6%, p <.01 [HC] vs. +15.2%, p =.01 [MA]) and decrements in FEV(1) (-8.0%, p <.01 [HC] vs. -3.2%, p <.05 [MA]) did not differ between the two groups. These data demonstrate significant differences between the interaction of ozone with RTLF antioxidants in MA and HC subjects. These responses and variations in basal antioxidant defense were not, however, useful predictive markers of group or individual responsiveness to ozone.     

Synthesis and in vitro evaluation of tetrahydroisoquinolinyl benzamides as ligands for sigma receptors

5-Bromo-N-[4-(6,7-dimethoxy-3,4-dihydro-1H-isoquinolin-2-yl)-butyl)]-2,3-dimethoxy-benzamide (1) is one of the most potent and selective sigma(2) receptor ligands reported to date. Previous structure-activity relationship studies of such tetrahydroisoquinolinyl benzamides have focused on the linker that connects the ring systems and the effects of benzamide ring substituents. The present study explores the effects of fusing methylene-, ethylene-, and propylenedioxy rings onto the tetrahydroisoquinoline in place of the two methoxy groups. These modifications decreased sigma(2) affinity by 8- to 12-fold, with no major differences noted with ring size. By contrast, the methylenedioxy analog showed a 10-fold greater sigma(1) affinity than 1, and progressively lower sigma(1) affinities were then noted with increasing ring size. We also opened the tetrahydroisoquinoline ring of 1 to study the effects of greater conformational fluidity on sigma receptor binding. The sigma(2) affinity of the open-ring compound decreased by 1700-fold, while sigma(1) affinity was not changed. Thus, a constrained tetrahydroisoquinoline ring system is key to the exceptional sigma(2) receptor binding affinity and selectivity of this active series.     

Effects of organism size and community composition on ecosystem functioning

We tested (1) if the size of dominant species influenced ecosystem functioning in food webs consisting of bacteria, algae, and protozoa; (2) whether those effects changed in importance through time; and (3) how those effects compared with differences in diversity among experimental food webs. We constructed food webs using two size fractions of organisms that differed in individual mass by approximately two orders of magnitude. We measured total biomass and respiration (total CO₂ production) as two aspects of ecosystem functioning. We also compared these size‐dependent patterns in functioning across two levels of species richness. Initially, organism size strongly influenced total community biomass. With time, however, biomass and respiration eventually converged in communities dominated by large or small species. We conclude that after sufficient time for community development any differences in ecosystem functioning resulted from differences in community composition, including species richness, but not the size of the dominant organisms.     

Using molecular markers with high mutation rates to obtain estimates of relative population size and to distinguish the effects of gene flow and mutation: a demonstration using data from endemic Mauritian skinks

We propose a method of analysing genetic data to obtain separate estimates of the size (N(p)) and migration rate (m(p)) for the sampled populations, without precise prior knowledge of mutation rates at each locus ( micro(L)). The effects of migration and mutation can be distinguished because high migration has the effect of reducing genetic differentiation across all loci, whereas a high mutation rate will only affect the locus in question. The method also takes account of any differences between the spectra of immigrant alleles and of new mutant alleles. If the genetic data come from a range of population sizes, and the loci have a range of mutation rates, it is possible to estimate the relative sizes of the different N(p) values, and likewise the m(p) and the micro(L). Microsatellite loci may also be particularly appropriate because loci with a high mutation rate can reach mutation-drift-migration equilibrium more quickly, and because the spectra of mutants arriving in a population can be particularly distinct from the immigrants. We demonstrate this principle using a microsatellite data set from Mauritian skinks. The method identifies low gene flow between a putative new species and populations of its sister species, whereas the differentiation of two other populations is attributed to small population size. These distinct interpretations were not readily apparent from conventional measures of genetic differentiation and gene diversity. When the method is evaluated using simulated data sets, it correctly distinguishes low gene flow from small population size. Loci that are not at mutation-migration-drift equilibrium can distort the parameter estimates slightly. We discuss strategies for detecting and overcoming this effect.     

The relationship between pollen grain size and progeny gender in dioecious Silene latifolia (Caryophyllaceae)

Summary Experiments and observations conducted during the past 90 years have provided conflicting evidence concerning the existence of a size difference between pollen grains containing an X chromosome (female-determining) and those containing a Y chromosome (maledetermining) in dioecious Silene latifolia. Were such a size difference to exist, this might explain, at least in part, the observation that X-bearing pollen tubes reach the ovary more quickly, on average, than Y-bearing pollen tubes. We tested for such a size difference by separating pollen collected from single anthers into three size classes: small, large, and random. Fruit set (number of pollinated flowers that set fruit) and seed set (number of seeds per capsule) did not differ for these three pollination treatments. Progeny sex ratios resulting from these three pollen size classes also did not differ significantly. Thus, pollen grain size is not affected by which of the two sex chromosomes is present. Our experiment is the first direct test of this relationship. Based on our results, size differences should not be invoked to explain competitive differences in male- and female-determining microgametophytes.     

Breeding ecology and seasonal abundance of the giant water bug Appasus japonicus (Heteroptera, Belostomatidae)

Males of the giant water bug Appasus (= Diplonychus) japonicus Vuillefroy (Belostomatidae: Heteroptera) carry egg masses on their back, but little is known about the relationship between seasonal abundance and breeding ecology of the species. In the present study, therefore, a field survey based on a mark-and-recapture census was carried out at three survey points within a rice paddy area (0.3 km²) where A. japonicus forms a meta-population in northern Okayama, Japan. We investigated the body size, seasonal abundance, dispersion, egg mass size (number of eggs within one egg mass), number of egg masses and the total eggs carried on the back of each male as fundamental parameters of the population and breeding. Significant differences in egg mass size, number of egg masses, and total number of eggs that males carried was found among the survey points. The present results suggested the possibility that the differences in breeding parameters of A. japonicus were influenced by differences in environmental factors among the microhabitats. These results are discussed in conjunction with previous reports on seasonal abundance and breeding systems in Belostomatidae bugs.     

Metabolism, body size and life span: a case study in evolutionarily divergent populations of the garter snake (Thamnophis elegans)

We present a case study of metabolism, life history and aging in the western terrestrial garter snake (Thamnophis elegans). Early research in the field supported the rate-of-living hypothesis as an explanation of aging, which was based on an apparent negative relationship between mass-specific metabolic rate and lifespan in endotherms. This hypothesis in its original form has not withstood additional tests and comparisons between the two main lineages of endotherms-birds and mammals, but there is still much to be discovered of the causative links among rate of oxygen consumption, physiology and life history, particularly in ectothermic reptiles. We present data that show adult short-lived snakes, from naturally occurring ecotypes of garter snakes, have higher mass-specific resting metabolic rates at any given body mass (metabolic intensity) across a series of normal activity temperatures (15-32°C). The short-lived ecotype in this geographic region reaches a larger body size, and has life-history traits that place it at the fast end of a pace-of-life continuum (fast growth, early maturation, high reproductive output) relative to individuals of the small-bodied long-lived ecotype. The difference between ecotypes in metabolic intensity, even after acclimation to identical conditions, may reflect evolutionary divergence and genetic differences between ecotypes. The difference in metabolic intensity is not, however, present at birth, so an alternative is that developmental environment may permanently influence metabolic rate and life history. Such developmental canalization could lead to altered gene expression via environmental influences on the epigenome and result in altered metabolic trajectories in the snakes' natural habitats.     

Environmental and genetic influences on queen and worker body size in the social wasp Vespula maculifrons

Many social insects exhibit morphologically distinct worker and queen castes that perform different functions. These functional differences may generate unique selection regimes operating on body size. For example, queens may be under directional selection for large body size, whereas directional selection on worker body size may be limited. Such contrasting selection pressures may differentially affect levels of genetic variation associated with size variation in the two castes. This study sought to determine if genetic effects underlying phenotypic differences varied between the worker and queen castes of the social wasp Vespula maculifrons. We predicted that directional selection would remove genetic variation associated with size differences in the queen caste, whereas a lack of directional selection would tend to maintain genetic variation associated with size differences in the worker caste. We thus (1) calculated broad and narrow sense heritabilities for several morphological traits, (2) examined whether some paternal genotypes produced more morphologically diverse offspring than others, and (3) determined whether trait size variation was associated with genetic variation within colonies. We found that few morphological traits were significantly heritable, indicating that little genetic variance for those traits existed within our study population. We also found that some patrilines produced more morphologically variable offspring than others, suggesting a role of genotype in phenotypic plasticity. And finally, no significant correlations between genetic diversity arising from multiple mating by queens within colonies and trait variation in either caste were found. Overall, our findings indicate a weak effect of genotype on both worker and queen body size variation and are suggestive of a large environmental influence on morphological trait size. Moreover, our results do not indicate that levels of genetic variation underlying size variation differ substantially between castes in this species.     

Investigations in plant commonness and rarity: a comparison of seed removal patterns in the widespread Jatropha standleyi and the endemic J. chamelensis (Euphorbiaceae)

During early August to late September 1998 we examined seed dispersal in the tree species Jatropha standleyi (widespread) and J. chamelensis (endemic; Euphorbiaceae) at the Estacion de Biologia Chamela, Jalisco, Mexico. Using general linear models, we found that seed removal from beneath the parental canopy did not differ between the two species and that seed removal was correlated with both seed availability on the ground and rodent predation. We inferred that seed removal was largely mediated by rodents and determined that if a seed was not removed within 4d (approx. 16% chance), it was highly unlikely to be removed at all (approx. 3.5% chance) for both species. We note that although differences in patterns of seed removal may not explain the observed differences in range size, differences between the two species in seed crop size arc similar to patterns found in other endemic/widespread species pairs.     

The morphological variation of the eggs and genital plates of two morphotypes of Triatoma protracta Uhler, 1894

The control of triatomine insects is necessary because these insects are the principal vectors of Trypanosoma cruzi, the agent of Chagas disease. Nevertheless, some of these vectors, such as Triatoma protracta, have not been studied adequately and their importance and taxonomic status has not yet been defined in detail and must be reevaluated in view of the continuing taxonomic uncertainties associated with the species. To help clarify the taxonomic status of T. protracta, the eggs and genital plates of two morphotypes were analyzed. Qualitative and quantitative morphological differences were observed in two morphotypes, designated T. p. protracta and T. p. nahuatlae according to Ryckman (1962). The morphotype T. p. protracta exhibited large and wide eggs with pores forming large padded polygonal structures, whereas the eggs of the morphotype T. p. nahuatlae were small and smooth. The size of the 9(th) genital urosternite was longer and wider in females in contrast to males in both morphotypes. However, these size differences were relatively greater in T. p. protracta. The high morphological variation found between the morphotypes of T. protracta suggests that they should be separated. Accordingly, it is probable that this group should be re-classified.