Estimation of parameters in large offspring number models and ratios of coalescence times

The ratio of singletons to the total number of segregating sites is used to estimate a reproduction parameter in a population model of large offspring numbers without having to jointly estimate the mutation rate. For neutral genetic variation, the ratio of singletons to the total number of segregating sites is equivalent to the ratio of total length of external branches to the total length of the gene genealogy. A multinomial maximum likelihood method that takes into account more frequency classes than just the singletons is developed to estimate the parameter of another large offspring number model. The performance of these methods with regard to sample size, mutation rate, and bias, is investigated by simulation. The expected value of the ratio of the total length of external branches to the total length of the whole tree is, using simulation, shown to decrease for the Kingman coalescent as sample size increases, but can increase or decrease, depending on parameter values, for Λ coalescents. Considering ratios of tree statistics, as opposed to considering lengths of various subtrees separately, can yield better insight into the dynamics of gene genealogies.     

Moulting of insect tracheae captured by light and electron-microscopy in the metathoracic femur of a third instar locust Locusta migratoria

The insect tracheal system is an air-filled branching network of internal tubing that functions to exchange respiratory gases between the tissues and the environment. The light and electron-micrographs presented in this study show tracheae in the process of moulting, captured from the metathoracic hopping femur of a juvenile third instar locust (Locusta migratoria). The images provide evidence for the detachment of the cuticular intima from the tracheal epithelial cells, the presence of moulting fluid between the new and old cuticle layers, and the withdrawal of the shed cuticular lining through larger upstream regions of the tracheal system during moulting. The micrographs also reveal that the cuticular intima of the fine terminal branches of the tracheal system is cast at ecdysis. Therefore, the hypothesis that tracheoles retain their cuticle lining at each moult may not apply to all insect species or developmental stages.     

A strong nucleotypic effect on the cell cycle regardless of ploidy level

Background and Aims: In published studies, positive relationships between nucleotypeand the duration of the mitotic cell cycle in angiosperms havebeen reported but the highest number of species analyzed wasapprox. 60. Here an analysis is presented of DNA C-values andcell cycle times in root apical meristems of angiosperms comprising110 measurements, including monocots and eudicots within a settemperature range, and encompassing an approx. 290-fold variationin DNA C-values. Methods: Data for 110 published cell cycle times of seedlings grown attemperatures between 20–25 °C were compared with DNAC-values (58 values for monocots and 52 for eudicots). Regressionanalyses were undertaken for all species, and separately formonocots and eudicots, diploids and polyploids, and annualsand perennials. Cell cycle times were plotted against the nuclearDNA C-values. Key Results: A positive relationship was observed between DNA C-value andcell cycle time for all species and for eudicots and monocotsseparately, regardless of the presence or absence of polyploidvalues. In this sample, among 52 eudicots the maximum cell cyclelength was 18 h, whereas the 58 monocot values ranged from 8–120h. There was a striking additional increase in cell cycle durationin perennial monocots with C-values greater than 25 pg. Indeed,the most powerful relationship between DNA C-value and cellcycle time and the widest range of cell cycle times was in perennialsregardless of ploidy level. Conclusions: DNA replication is identified as a rate limiting step in thecell cycle, the flexibility of DNA replication is explored,and we speculate on how the licensing of initiation points ofDNA replication may be a responsive component of the positivenucleotypic effect of C-value on the duration of the mitoticcell cycle.     

Measuring agreement of multivariate discrete survival times using a modified weighted kappa coefficient

Summary .  Assessing agreement is often of interest in clinical studies to evaluate the similarity of measurements produced by different raters or methods on the same subjects. We present a modified weighted kappa coefficient to measure agreement between bivariate discrete survival times. The proposed kappa coefficient accommodates censoring by redistributing the mass of censored observations within the grid where the unobserved events may potentially happen. A generalized modified weighted kappa is proposed for multivariate discrete survival times. We estimate the modified kappa coefficients nonparametrically through a multivariate survival function estimator. The asymptotic properties of the kappa estimators are established and the performance of the estimators are examined through simulation studies of bivariate and trivariate survival times. We illustrate the application of the modified kappa coefficient in the presence of censored observations with data from a prostate cancer study.     

Temporal patterns of diversification and microendemism in Eastern Highland endemic barcheek darters (Percidae: Etheostomatinae)

Eastern North America is the location of the world's most species-rich temperate freshwater fish fauna. Hypotheses regarding the geographic and temporal scale of teleost diversification in this region have not been broadly investigated using absolute divergence time estimates among the constituent lineages. This study used time-calibrated molecular phylogenies estimated from mitochondrial and nuclear genes to investigate the temporal and geographic signatures of diversification within barcheek darters, a clade of allopatrically distributed species endemic to the Eastern Highlands. Results from divergence time estimates using an uncorrelated lognormal model suggest that the barcheek darters are an ancient group with a crown node estimate of 16.3 mya, 95% highest posterior density (HPD): [12.4, 20.5], and the clade is characterized by substantial intraspecific divergence times within several species. In particular, the Caney Fork endemic Etheostoma basilare comprises five strongly supported and deeply divergent clades with a most recent common ancestor estimated at 8.0 mya, 95% HPD: [5.6, 10.7]. These results are concordant with the hypothesis that geologically stable areas of eastern North America have facilitated both the generation and preservation of lineages across a substantial breadth of evolutionary time, and that allopatric speciation in darters has occurred at much smaller spatial scales than previously realized.     

Molting in workers of the Formosan subterranean termite Coptotermes formosanus

The Formosan subterranean termite, Coptotermes formosanus, with its huge colonies, is a major urban pest in several southern states and Hawaii as well as in South Asia. Because of their cryptic nature (underground habitat) and very long life cycle, not much is known about molting in termite workers. In C. formosanus, the workers stop foraging and lose their gut fauna, respectively, approximately 10 and 5 days prior to ecdysis. In any given colony an average of 1.01% (range 0.6-1.8) of the workers were found to molt each day under laboratory conditions. Workers destined to molt become sluggish and their head capsules develop a mottled texture one day prior to ecdysis. Ecdysis was generally accomplished with the assistance of other workers, which also fed on the exuviae. Immediately after molting worker mandibles were light pink in color and became fully melanized approximately two days later. Gut fauna were acquired on the fourth day after molting. Flagellates were transferred as small encysted cells from other workers through proctodeal feeding. Juvenile hormone III titer ranged between 30-41 pg/mg bodyweight in all stages except in workers sampled 6 days prior to ecdysis. In these workers the titer was 80.5 pg/mg. The high juvenile hormones (JH) titer may also be involved in causing defaunation. Ecdysteroid titer increased from 2.1 pg/mg in non-molting workers to 359.5 and 332.4 pg/mg one and two days following defaunation, respectively. There was a second smaller peak two days prior to ecdysis.     

Lineages-through-time plots of neutral models for speciation

Drawing inferences about macroevolutionary processes from phylogenetic trees is a fundamental challenge in evolutionary biology. Understanding stochastic models for speciation is an essential step in solving this challenge. We consider a neutral class of stochastic models for speciation, the constant rate birth-death process. For trees with n extant species - which might be derived from bigger trees via random taxon sampling - we calculate the expected time of the kth speciation event (k=1,...,n-1). Further, for a tree with n extant species, we calculate the density and expectation for the number of lineages at any time between the origin of the process and the present. With the developed methods, expected lineages-through-time (LTT) plots can be drawn analytically. The effect of random taxon sampling on LTT plots is discussed.     

Dated historical biogeography of the temperate Loliinae (Poaceae, Pooideae) grasses in the northern and southern hemispheres

Divergence times and biogeographical analyses have been conducted within the Loliinae, one of the largest subtribes of temperate grasses. New sequence data from representatives of the almost unexplored New World, New Zealand, and Eastern Asian centres were added to those of the panMediterranean region and used to reconstruct the phylogeny of the group and to calculate the times of lineage-splitting using Bayesian approaches. The traditional separation between broad-leaved and fine-leaved Festuca species was still maintained, though several new broad-leaved lineages fell within the fine-leaved clade or were placed in an unsupported intermediate position. A strong biogeographical signal was detected for several Asian-American, American, Neozeylandic, and Macaronesian clades with different affinities to both the broad and the fine-leaved Festuca. Bayesian estimates of divergence and dispersal-vicariance analyses indicate that the broad-leaved and fine-leaved Loliinae likely originated in the Miocene (13My) in the panMediterranean-SW Asian region and then expanded towards C and E Asia from where they colonized the New World. Further expansions in America (10-3.8My) showed a predominant migratory route from North to South (N America<-->the Andes<-->Patagonia). This late Tertiary scenario of successive colonizations and secondary polyploid radiations in the southern hemisphere from the northern hemisphere was accompanied by occasional transcontinental long-distance dispersal events between South America and New Zealand. Multiple Pliocene dispersal events (3.6-2.5My) from the near SW European and NW African continents gave rise to the Macaronesian Loliinae flora, while a more recent Pleistocene origin (2-1My) is hypothesized for the high polyploid lineages that successfully colonized newly deglaciated areas in both hemispheres.     

Timing and ecdysteroid regulation of the molt in last instar greenhouse whiteflies (Trialeurodes vaporariorum)

A system of markers has been devised to track the development of 3rd and 4th instar/pharate adult greenhouse whiteflies. Instars were identified based on measurements of body width and body length. Depending upon the host plant, the product of the two measurements was exceptionally useful in distinguishing between instars. Body depth was used to divide the 3rd instar into eight stages and body depth and color and appearance of the developing adult eye were used to divide the 4th instar/pharate adult into nine stages. Under conditions of L:D 16:8 and a temperature of 26±2°C, the body depth of 3rd instars reared on greenbean increased from 0.025 (stage 1) to 0.2 mm (stage 8) and the instar duration was approximately 3 days. The body depth of 4th instars increased from approximately 0.1±0.02 (Stage 1) to 0.3±0.03 mm (Stage 5) and then remained constant or decreased slightly during adult development. Ecdysteroid titers peaked at approximately 120 fg/μg protein during Stages 3 through 6 of the 4th instar. Based on an external examination of developing 4th instars and the fluctuations in ecdysteroid titer, it appears that adult development is initiated in Stage 4 or 5 4th instars. Results from histological studies support this view. In Stage 4 nymphs, a subtle change was observed in the corneagenous cells of the eye. However, most Stage 4 4th instars possessed wing development characteristic of earlier, immature stages. In all Stage 5 insects, wing development had been initiated and the corneagenous cells had become quite distinct. In Stage 6 whiteflies, the wing buds were deeply folded and by Stage 7, spines were observed on the new cuticle, indicating that the adult cuticle was well-formed by this stage. Our study is the first to investigate the timing and regulation of the molt, to monitor ecdysteroid titers in precisely staged 4th instar whiteflies and to examine the internal anatomical changes associated with metamorphosis in these tiny homopteran insects.