Individual Partitions Research Articles

Effect of sustained elevated temperature prior to amplification on template copy number estimation using digital polymerase chain reaction

Digital polymerase chain reaction (dPCR) has the potential to enable accurate quantification of target DNA copy number provided that all target DNA molecules are successfully amplified. Following duplex dPCR analysis from a linear DNA target sequence that contains single copies of two independent template sequences, we have observed that amplification of both templates in a single partition does not always occur. To investigate this finding, we heated the target DNA solution to 95 °C for increasing time intervals and then immediately chilled on ice prior to preparing the dPCR mix. We observed an exponential decline in estimated copy number (R(2)≥ 0.98) of the two template sequences when amplified from either a linearized plasmid or a 388 base pair (bp) amplicon containing the same two template sequences. The distribution of amplifiable templates and the final concentration (copies per µL) were both affected by heat treatment of the samples at 95 °C from 0 s to 30 min. The proportion of target sequences from which only one of the two templates was amplified in a single partition (either 1507 or hmg only) increased over time, while the proportion of target sequences where both templates were amplified (1507 and hmg) in each individual partition declined rapidly from 94% to 52% (plasmid) and 88% to 31% (388 bp amplicon) suggesting an increase in number of targets from which both templates no longer amplify. A 10 min incubation at 95 °C reduced the initial amplifiable template concentration of the plasmid and the 388 bp amplicon by 59% and 91%, respectively. To determine if a similar decrease in amplifiable target occurs during the default pre-activation step of typical PCR amplification protocol, we used mastermixes with a 20 s or 10 min hot-start. The choice of mastermix and consequent pre-activation time did not affect the estimated plasmid concentration. Therefore, we conclude that prolonged exposure of this DNA template to elevated temperatures could lead to significant bias in dPCR measurements. However, care must be taken when designing PCR and non-PCR based experiments by reducing exposure of the DNA template to sustained elevated temperatures in order to improve accuracy in copy number estimation and concentration determination.

Determination of partition coefficient and analysis of nitrophenols by three-phase liquid-phase microextraction coupled with capillary electrophoresis

A three-phase hollow fiber liquid-phase microextraction method coupled with CE was developed and used for the determination of partition coefficients and analysis of selected nitrophenols in water samples. The selected nitrophenols were extracted from 14 mL of aqueous solution (donor solution) with the pH adjusted to pH 3 into an organic phase (1-octanol) immobilized in the pores of the hollow fiber and finally backextracted into 40.0 microL of the acceptor phase (NaOH) at pH 12.0 located inside the lumen of the hollow fiber. The extractions were carried out under the following optimum conditions: donor solution, 0.05 M H(3)PO(4), pH 3.0; organic solvent, 1-octanol; acceptor solution, 40 microL of 0.1 M NaOH, pH 12.0; agitation rate, 1050 rpm; extraction time, 15 min. Under optimized conditions, the calibration curves for the analytes were linear in the range of 0.05-0.30 mg/L with r(2)>0.9900 and LODs were in the range of 0.01-0.04 mg/L with RSDs of 1.25-2.32%. Excellent enrichment factors of up to 398-folds were obtained. It was found that the partition coefficient (K(a/d)) values were high for 2-nitrophenol, 3-nitrophenol, 4-nitrophenol, 2,4-dinitrophenol and 2,6-dinitrophenol and that the individual partition coefficients (K(org/d) and K(a/org)) promoted efficient simultaneous extraction from the donor through the organic phase and further into the acceptor phase. The developed method was successfully applied for the analysis of water samples.

Modeling the environmental fate of perfluorooctanoic acid and perfluorooctanoate: An investigation of the role of individual species partitioning

A multimedia multi-species environmental fate model was developed for the conjugate pair perfluorooctanoic acid (PFOA):perfluorooctanoate (PFO). The model allows assessment of the relative contribution of each individual species, in equilibrium with each other, to the overall environmental movement of the pair. The Lake Ontario (Canada/USA) watershed system was selected for this investigation and is simulated in a single-region, seven-compartment model, including a water surface microlayer, and aqueous aerosol generation and redeposition. Results indicate that in the equilibrated presence of both PFOA and PFO, the environmental fate of the pair can be accomplished by consideration of the physical properties of the neutral acid, which govern the intermedia distribution of the pair, coupled with processes of media advection, such as air or water flow. The role of the anion, while the most populous species in the aqueous phase, appears merely to be as a source of the neutral acid for subsequent partitioning. Thus, when only the bulk aqueous phase anion concentrations are of interest a multimedia fate model is not required because these concentrations are largely predictable from the magnitude of emissions to and the advection of the phase. With neutral species partitioning, all local field measurement concentrations of the conjugate pair, PFO(A), are explained by the model to within approximately an order of magnitude, with the exception of lake sediment solids. Model results indicate that bulk aqueous phase PFO acts as a net source for PFOA to the atmosphere, where it may be subject to long-range transport (LRT). Initial calculations suggest an atmospheric LRT potential for PFO(A) of thousands of kilometers, rendering it comparable to hexachlorobenzene.

Amalgamation of partitions from multiple segmentation bases: A comparison of non-model-based and model-based methods

The segmentation of customers on multiple bases is a pervasive problem in marketing research. For example, segmentation service providers partition customers using a variety of demographic and psychographic characteristics, as well as an array of consumption attributes such as brand loyalty, switching behavior, and product/service satisfaction. Unfortunately, the partitions obtained from multiple bases are often not in good agreement with one another, making effective segmentation a difficult managerial task. Therefore, the construction of segments using multiple independent bases often results in a need to establish a partition that represents an amalgamation or consensus of the individual partitions. In this paper, we compare three methods for finding a consensus partition. The first two methods are deterministic, do not use a statistical model in the development of the consensus partition, and are representative of methods used in commercial settings, whereas the third method is based on finite mixture modeling. In a large-scale simulation experiment the finite mixture model yielded better average recovery of holdout (validation) partitions than its non-model-based competitors. This result calls for important changes in the current practice of segmentation service providers that group customers for a variety of managerial goals related to the design and marketing of products and services.

Screening-level ecological and human health risk assessment of polycyclic aromatic hydrocarbons in stormwater detention pond sediments of Coastal South Carolina, USA

Screening-level ecological and human health assessments were performed for polycyclic aromatic hydrocarbon (PAH) contamination in the sediments of 19 stormwater detention ponds located in coastal South Carolina. For ecological screening benchmarks, we used threshold and probable effect concentrations (TEC and PEC) derived from consensus-based sediment quality guidelines for individual PAH analytes and equilibrium partitioning sediment benchmarks-toxic units (SigmaESB-TU) derived for PAH mixtures. For human health benchmarks, we used preliminary remediation goals (PRGs). Sediments of five stormwater ponds (four commercial ponds and one residential pond with a large drainage area) exceeded PEC values for several PAH analytes and the SigmaESB-TU safe value of 1 for PAH mixtures. These same five stormwater ponds also exceeded the PRG values for five carcinogenic PAH analytes. These results suggest that the PAH levels in sediments from certain commercial and residential ponds have the potential to pose moderate to high risks for adverse, chronic effects to benthic organisms in situ and an increased risk of cancer to humans ex situ following excavation and on-site disposal. We recommend that sediment from these stormwater ponds be tested prior to excavation to determine the appropriate method of disposal. We also recommend that regulatory agencies enforce guidelines for periodic sediment removal as this should reduce both in situ and ex situ risks resulting from sediment PAH exposure.

Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae)

The pantherine lineage of cats diverged from the remainder of modern Felidae less than 11 million years ago and consists of the five big cats of the genus Panthera, the lion, tiger, jaguar, leopard, and snow leopard, as well as the closely related clouded leopard. A significant problem exists with respect to the precise phylogeny of these highly threatened great cats. Despite multiple publications on the subject, no two molecular studies have reconstructed Panthera with the same topology. These evolutionary relationships remain unresolved partially due to the recent and rapid radiation of pantherines in the Pliocene, individual speciation events occurring within less than 1 million years, and probable introgression between lineages following their divergence. We provide an alternative, highly supported interpretation of the evolutionary history of the pantherine lineage using novel and published DNA sequence data from the autosomes, both sex chromosomes and the mitochondrial genome. New sequences were generated for 39 single-copy regions of the felid Y chromosome, as well as four mitochondrial and four autosomal gene segments, totaling 28.7 kb. Phylogenetic analysis of these new data, combined with all published data in GenBank, highlighted the prevalence of phylogenetic disparities stemming either from the amplification of a mitochondrial to nuclear translocation event (numt), or errors in species identification. Our 47.6 kb combined dataset was analyzed as a supermatrix and with respect to individual partitions using maximum likelihood and Bayesian phylogenetic inference, in conjunction with Bayesian Estimation of Species Trees (BEST) which accounts for heterogeneous gene histories. Our results yield a robust consensus topology supporting the monophyly of lion and leopard, with jaguar sister to these species, as well as a sister species relationship of tiger and snow leopard. These results highlight new avenues for the study of speciation genomics and understanding the historical events surrounding the origin of the members of this lineage.

Patterns of habitat affinity and Austral/Holarctic parallelism in dictynoid spiders (Araneae:Entelegynae)

The ability to survive in a terrestrial environment was a major evolutionary hurdle for animals that, once passed, allowed the diversification of most arthropod and vertebrate lineages. Return to a truly aquatic lifestyle has occurred only rarely among terrestrial lineages, and is generally associated with modifications of the respiratory system to conserve oxygen and allow extended periods of apnea. Among chelicerates, in particular spiders, where the circulatory system also serves as a hydrostatic skeleton, very few taxa have exploited aquatic environments, though these environments are abundant and range from freshwater ponds to the marine intertidal and relictual (salt) lakes. The traditional systematic positions of the taxa inhabiting these environments are controversial. Partitioned Bayesian analysis using a doublet model for stems in the nearly complete 18S rRNA gene (~1800 nt) and in the D2 and D3 regions of the 28S rRNA gene (~690 nt), and standard models for loops and full protein-coding histone H3 (349 nt) partitions (totalling 3133 bp when aligned) of dictynoid spiders and related lineages revealed that the only truly aquatic spider species, Argyroneta aquatica (Clerck, 1767) (Cybaeidae Banks, 1892), belongs in a clade containing other taxa with unusual habitat affinities related to an aquatic existence, including occupation of semi-aquatic (intertidal) areas (Desidae Pocock, 1985: Paratheuma spp.) and highly alkaline salt-crusts (Dictynidae O. Pickard-Cambridge, 1871: Saltonia incerta (Banks, 1898)). In a contrasting pattern, other spiders that also occupy intertidal zones, including some other members of the family Desidae (Desis spp., Badumna longinqua (L. Koch, 1867)), are an independently derived clade found primarily in the southern hemisphere. Use of the doublet model reduced some branch-support values in the single-gene trees for rRNA data, but resulted in a robust combined-data phylogeny from 18S rRNA, 28S rRNA, and histone H3. This combination of results – reduction in support in single-gene trees and gain in support in combined-data trees –is consistent with use of the doublet model reducing problematic signal from non-independent base pairs in individual data partitions, resulting in improved resolution in the combined-data analyses.

Non-Bossy Social Classification

We consider the problem of how societies should be partitioned into classes if individuals express their views about who should be put with whom in the same class. A non-bossiness condition makes the social aggregator dependent only on those cells of the individual partitions the society members classify themselves in. This information is used to construct for each profile of views an opinion graph. By means of natural sovereignty and liberalism requirements, we characterize the non-bossy aggregators generating partitions in which the social classes are refinements of the connected components in the opinion graph.

Distinct-value synopses for multiset operations

The task of estimating the number of distinct values (DVs) in a large dataset arises in a wide variety of settings in computer science and elsewhere. We provide DV estimation techniques for the case in which the dataset of interest is split into partitions. We create for each partition a synopsis that can be used to estimate the number of DVs in the partition. By combining and extending a number of results in the literature, we obtain both suitable synopses and DV estimators. The synopses can be created in parallel, and can be easily combined to yield synopses and DV estimates for "compound" partitions that are created from the base partitions via arbitrary multiset union, intersection, or difference operations. Our synopses can also handle deletions of individual partition elements. We prove that our DV estimators are unbiased, provide error bounds, and show how to select synopsis sizes in order to achieve a desired estimation accuracy. Experiments and theory indicate that our synopses and estimators lead to lower computational costs and more accurate DV estimates than previous approaches.

A whole-genome phylogeny of the family Pasteurellaceae

A phylogenomic approach was used to generate an amino acid phylogeny for 12 whole genomes representing 10 species in the family Pasteurellaceae. Orthology of genes was determined using an approach similar to OrthologID (http://nypg.bio.nyu.edu/orthologid/about.html) and resulted in the generation of a matrix with 3130 genes with 1,194,615 aligned amino acid characters of which 239,504 characters are phylogenetically informative. Phylogenetic analysis of the concatenated matrix using all standard approaches (maximum parsimony, maximum likelihood, and Bayesian analysis) results in a single extremely robust phylogenetic hypothesis for the species examined in this study. Remarkably, no single gene partition gives the same tree as the concatenated analysis. By analyzing partitioned support in the data matrix, we show that there is very little negative support emanating from individual gene partitions to suggest that the concatenated hypothesis is not tenable. The large number of characters in the matrix allows us to test hypotheses concerning missing data and character number in phylogenomic studies, and we conclude that matrices constructed using genome level information are very robust to missing data. We show that a very large number of concatenated gene sequences (>160) are needed to reliably obtain the same topology as the overall analysis.

Relationships of self-reported physical activity domains with accelerometry recordings in French adults

The objective was to examine the relationships of self-reported physical activity (PA) by domain (leisure, occupational, other) with PA and sedentary time as measured objectively by accelerometry. Subjects were adults with low habitual PA levels from a community in northern France. Among subjects in the lowest tertile of a PA score from a screening questionnaire, 160 (37% males, age: 41.0 +/- 10.8 years, BMI: 25.1 +/- 4.1 kg/m(2), mean +/- SD) completed a detailed instrument (Modifiable Activity Questionnaire), and wore an accelerometer (Actigraph) for seven consecutive days. Relationships between questionnaire domains (occupational, leisure, and "non-occupational non-leisure") and accelerometry measures (total activity and sedentary time) were assessed using Spearman correlation coefficients. In this population, the highest contributor to total reported PA (h/week) was occupational PA. Time spent in non-occupational non-leisure PA ranked second in women and third in men. The most frequent non-occupational non-leisure PA were shopping and household chores. In women, non-occupational non-leisure PA contributed more than occupational or leisure-time PA to total PA energy expenditure (median: 18.0, 9.1, and 4.9 MET-h/week, respectively). Total PA by accelerometry (count/day) was correlated to leisure-time PA in women (r = 0.22, P < 0.05) and to occupational (r = 0.43, P < 0.01) and total reported PA (r = 0.39, P < 0.01) in men (all in MET-h/week). There was an inverse relationship between accelerometry sedentary time (h/day) and non-occupational non-leisure PA (MET-h/week, r = -0.30, P < 0.001). These findings indicate the importance of assessing non-occupational non-leisure PA for a better understanding of how individuals partition their time between active or sedentary occupations.

Temperature dependence of yields of secondary organic aerosols from the ozonolysis of &amp;lt;i&amp;gt;α&amp;lt;/i&amp;gt;-pinene and limonene

Abstract. Secondary organic aerosol (SOA) formation has been investigated as a function of temperature and humidity for the ozone-initiated reaction of the two monoterpenes α-pinene (243–313 K) and limonene (253–313 K) using the 84.5 m3 aerosol chamber AIDA. This paper gives an overview of the measurements done and presents parameters specifically useful for aerosol yield calculations. The ozonolysis reaction, selected oxidation products and subsequent aerosol formation were followed using several analytical techniques for both gas and condensed phase characterisation. The effective densities of the SOA were determined by comparing mass and volume size distributions to (1.25±0.10) g cm−3 for α-pinene and (1.3±0.2) g cm−3 for limonene. The detailed aerosol dynamics code COSIMA-SOA proved to be essential for a comprehensive evaluation of the experimental results and for providing parameterisations directly applicable within atmospheric models. The COSIMA-assisted analysis succeeded to reproduce the observed time evolutions of SOA total mass, number and size distributions by adjusting the following properties of two oxidation product proxies: individual yield parameters (αi), partitioning coefficients (Ki), vapour pressures (pi) and effective accommodation coefficients (γi). For these properties temperature dependences were derived and parameterised. Vapour pressures and partitioning coefficients followed classical Clausius – Clapeyron temperature dependences. From this relationship enthalpies of vaporisation were derived for the two more and less volatile product proxies of α-pinene: (59±8) kJ mol−1 and (24±9) kJ mol−1, and limonene: (55±14) kJ mol−1 and (25±12) kJ mol−1. The more volatile proxy components had a notably low enthalpy of vaporisation while the less volatile proxy components gave enthalpies of vaporisation comparable with those of typical products from α-pinene oxidation, e.g. pinonaldehyde and pinonic acid.

Prediction of Hofmeister ion effects on biopolymer processes

At moderate to high concentrations, salt ions exert a wide range of effects on protein folding and other protein processes, from extremely destabilizing (GuH+, SCN-) to very stabilizing (SO42-). The Hofmeister series is a qualitative ranking of these effects, originally based on the effectiveness of salts as protein precipitants and subsequently observed for other processes including creating air-water surface and dissolving hydrocarbons in water. Recently surface spectroscopy, molecular dynamics simulations and molecular thermodynamic analysis of surface tension and model compound solubility data have all provided evidence that local accumulation or exclusion of individual salt ions, relative to bulk concentrations, is responsible for their Hofmeister effects. In particular, application of a novel two-domain salt ion partitioning model (SPM) to analyze effects of Hofmeister salts on the surface tension of water and on hydrocarbon and peptide solubility (Pegram & Record, J. Phys. Chem. B 112, 9428 (2008); 111, 5411 (2007)) provides a quantitative molecular thermodynamic description of the individual partitioning of salt cations and anions at uncharged interfaces, with predictive capability. This analysis shows that the Hofmeister rank order of ions arises from their interactions with nonpolar surface. Surface-bulk partition coefficients of ions obtained from hydrocarbon and amide model compound solubility data, together with a coarse-grained description of functional groups that make up molecular surfaces, allow the quantitative prediction of Hofmeister (noncoulombic) salt effects on micelle formation, protein folding, protein crystallization and DNA helix formation. This work is supported by NIH GM47022.

Phylogenetic relationships within the Cimicomorpha (Hemiptera: Heteroptera): a total‐evidence analysis

AbstractA phylogenetic analysis for the Cimicomorpha was conducted using 92 taxa, including eight outgroups and six species of Thaumastocoridae. Density of taxon sampling allows for tests of relationships at the family level for most taxa, whereas in the Miridae denser sampling allows for doing so on the tribal level. This level of sampling also corresponds with the availability of testable published hypotheses of relationships. Morphological data for 73 characters are coded for all taxa. Approximately 3500 base pairs of DNA were sequenced for the following gene regions for 83 taxa: 16S rDNA, 18S rDNA, 28S rDNA and COI. Results are presented for analysis of morphological data, individual molecular partitions, combined molecular data, combined morphological and molecular data for 83 taxa and combined morphological and molecular data for 92 taxa. Analyses of morphological data were performed using the parsimony programsnonaandpiwe: molecular and combined data were analysed using direct optimization with the programpoy. Major conclusions of the present study include recognition of the following monophyletic groups: The Geocorisae is a monophyletic group. The monophyly of the Cimicomorpha – including Thaumastocoridae – is not supported in most analyses. The Reduviidae is monophyletic, with the Phymatinae Complex being the sister‐group of the remaining subfamilies. The circumscription of the Cimiciformes is altered from the prior conception of Schuh and Štys to also include the Joppeicidae, Microphysidae and Velocipedidae, as well as the recently described family Curaliidae; the monophyly of the Cimiciformes is supported in most analyses; the Cimiciformes is treated as the sister‐group of the Miroidea in most analyses. The monophyly of the Cimicoidea, including Curaliidae, is supported in all analyses including molecular data, whereas Curaliidae is treated as a more basal cimiciform in all other analyses. The monophyly and placement of the Thaumastocoridae is ambiguous across the range of analyses, and the monophyly of the Miroidea sensu Schuh and Štys receives limited support in the combined analyses of morphology + molecular data. The Tingidae and Miridae are each monophyletic and together almost invariably form a monophyletic group. Within the Miridae, several inclusive monophyletic groups at the subfamily/tribal level are more or less consistently recognized when molecular data are included; however, the interrelationships of the subfamilies vary substantially across the range of analyses. Of the individual molecular partitions, only 18S rDNA shows significant congruence with combined analyses of morphological, combined molecular or combined morphological and molecular data. Scenarios are discussed for the evolution of the metathoracic scent‐efferent system and the origin of the fossula spongiosa.

Morphology versus molecules: the phylogenetic relationships of Sepsidae (Diptera: Cyclorrhapha) based on morphology and DNA sequence data from ten genes.

The Sepsidae is, with approximately 300 described species, a relatively small family of cyclorrhaphan flies whose behaviour, morphology, and development have been extensively studied. However, currently the only available tree for Sepsidae is more than 10 years old and was based entirely on morphological characters. Here, we present the results of parsimony and Bayesian analyses based on 75 species, ten genes, and morphology. Parsimony and Bayesian analyses produce largely congruent and well-supported topologies regardless of whether indels are coded as 5th character states, as missing values, or all sites with indels are removed. The tree confirms the monophyly of Sepsidae and identifies the Ropalomeridae as its sister group. With regard to higher-level relationships, we identify widespread conflict between the morphological and the DNA sequence data. The proposed hypothesis based on both partitions largely reflects the signal in the molecular data. Particularly surprising is the rejection of two relationship hypotheses with strong morphological support, namely the sister group relationship between Orygma and the remaining Sepsidae and the monophyly of the Sepsis species group. Our partitioned Bremer support (PBS) analyses imply that indel coding has a stronger effect on the relative performance of individual gene partitions than the exclusion of alignment-ambiguous sequences or the location of a gene on the mitochondrial or nuclear genome. However, these analyses also reveal unexpectedly strong fluctuations in PBS values given that indel treatment has only a minor effect on tree topology and jacknife support. These unexpected fluctuations highlight the need for a comparative study across multiple data sets that investigates the influence of conflict and indel treatment on PBS values. © The Willi Hennig Society 2008.

MAkE: Multiobjective algorithm for k-way equipartitioning of a point set

The classical problem of partitioning a given set of points, has applications in several areas such as facility location, scattered network, and in hierarchical design of VLSI circuits. While equipartitioning is traditionally associated with the single objective of minimum cutcost, the above application areas appear to demand more. In this paper, we introduce the problem of multiobjective k-way equipartitioning of a point set. Brief discussions on the above applications are followed by their generic formulation as a multiobjective k-way equipartitioning problem of a given point set. The non-commensurate multiobjective criteria addressed include (i) minimizing overall areas of the partitions, (ii) maximizing area of the individual partitions, (iii) minimizing the total compactness of the partitions, and (iv) minimizing the total geometric diversity of the obtained partitions. Since this optimization problem is computationally expensive in time and space, a technique based on genetic algorithm is proposed in order to obtain high quality results. Crossover and mutation operators specific to the k-way equipartitioning problem, have been designed and a new greedy operator named compaction is proposed to accelerate convergence. To illustrate the utility of the proposed formulation and the algorithm, a problem in VLSI layout design is considered. Results on synthetic data sets as well as those extracted from layouts of benchmark circuits demonstrate the effectiveness of the proposed multiobjective approach.

Additive Action of Two or More Solutes on Lipid Membranes

A wide variety of biological processes, pharmaceutical applications, and technical procedures is based on the combined action of two or more soluble compounds to perturb, permeabilize, or lyse biological membranes. Here we present a general model describing the additive action of solutes on the properties of membranes or micelles. The onset and completion of membrane solubilization induced by two surfactants (lauryl maltoside, with nonyl maltoside, octyl glucoside, or CHAPS, respectively) are very well described by our model on the basis of their individual partition coefficients, cmc's, and critical mole ratios R e sat and R e sol as detected by isothermal titration calorimetry. This suggests that the thermodynamic phase transition is governed by a single parameter (e.g., spontaneous curvature) in spite of the complexity of structural changes. Such surfactant mixtures show unique features such as nonlinear solubilization boundaries and concentration-dependent effective partition coefficients. Other phenomena such as membrane leakage are predicted to obey additive action if the solutes act via the same mechanism (e.g., toroidal pore formation) but deviate from the model in the case of independent, synergistic, or antagonistic action.

Morphology, Paleontology, and Placental Mammal Phylogeny

Placental mammals constitute the most intensively studied large clade of organisms. Deciphering their relationships has important implications not only to understand evolutionary processes (Bininda-Emonds et al., 2007) but also to inform many aspects of biomedical research (Springer and Murphy, 2007). Springer et al. (2007) have recently discussed limitations of morphological analysis of placental phylogeny compared with reconstructions based on molecular data. They presented a pessimistic view of the potential of morphological characters for use in high-level placental mammal phylogeny reconstruction, as the morphological data set they scrutinized (from Asher et al., 2003) does not recover the four major clades of mammals (Afrotheria, Xenarthra, Laurasiatheria, and Euarchontoglires) that these authors regard as overwhelmingly supported. In their contribution to the recurring debate on the “adequacy of morphology” (from their title), Springer et al. (2007) have provided empirical data to support their claims of the inadequacy of a morphological data set for resolving high-level mammalian phylogeny. Here, we would like to address several issues relevant to the arguments of Springer et al., including (1) their use of congruence of individual partitions to a “true” tree; (2) their generalization across morphological data sets based on their evaluation of one matrix; (3) their emulation of extinction as a heuristic tool; and (4) the role of paleontology and neontology in eutherian systematics. We end our commentary by discussing how “morphology” (comprising both paleontological and neontological characters) has not yet been fully exploited as a source of data for phylogenetic research.

How Accurate Are Approximate Methods for Evaluating Partition Functions for Hindered Internal Rotations?

The accuracy of several low-cost methods (harmonic oscillator approximation, CT-Comega, SR-TDPPI-HS, and TDPPI-HS) for calculating one-dimensional hindered rotor (1D-HR) partition functions is assessed for a test set of 644 rotations in 104 organic molecules, using full torsional eigenvalue summation (TES) as a benchmark. For methods requiring full rotational potentials, the effect of the resolution at which the rotational potential was calculated was also assessed. Although lower-cost methods such as Pitzer's Tables are appropriate when potentials can be adequately described by simple cosine curves, these were found to show large errors (as much as 3 orders of magnitude) for non-cosine curve potentials. In those cases, it is found that the TDPPI-HS method in conjunction with a potential compiled at a resolution of 60 degrees offers the best compromise between accuracy and computational expense. It can reproduce the benchmark values of the partition functions for an individual mode to within a factor of 2; its average error is just of a factor of 1.08. The corresponding error in the overall internal rotational partition functions of the molecules studied is less than a factor of 4 in all cases. Excellent cost-effective performance is also offered by CT-Comega, which requires only the geometries, energies, and frequencies of the distinguishable minima in the potential. With this method the geometric mean error in individual partition functions is 1.14, the maximum error is a modest 2.98 and the resulting error in the total 1D-HR partition function of a molecule is less than a factor of 5 in all cases.

A phylogenetic study of the ‘bombycoid complex’ (Lepidoptera) using five protein‐coding nuclear genes, with comments on the problem of macrolepidopteran phylogeny

Abstract This study had two aims. First, we tested the monophyly of and relationships within the ‘bombycoid complex’, an assembly of approximately 5300 species postulated by Minet to represent 12 families in three superfamilies, by sequencing five protein‐coding nuclear gene regions (CAD, DDC, enolase, period, wingless; approximately 6750 bp total) in 66 representatives of most of the subfamilies and tribes. Second, we sought initial evidence on the utility of these genes for estimating relationships among Macrolepidoptera more broadly (11 superfamilies total), by adding representatives of eight families from four other superfamilies, and by assessing the phylogenetic information content of the individual genes and partitions thereof. Analysis of the combined data by likelihood and parsimony upholds monophyly for the bombycoid complex and for Bombycoidea sensu stricto (includes Anthelidae, see below), but with weak bootstrap support. Minet’s assignment of Phiditiinae to Bombycoidea rather than to Noctuoidea is strongly upheld, but Anthelidae, placed in Lasiocampoidea by Minet, group securely within Bombycoidea sensu stricto. Within the latter, the basal split segregates a strongly supported ‘BALE’ group [Apatelodinae + (Eupterotidae + (Brahmaeidae + Lemoniidae))]. The remaining families form a consistently but weakly supported clade, within which the basal split segregates the very strongly supported ‘CAPOPEM’ group [Carthaeidae, Anthelidae, Phiditiinae, (Prismostictini + (Endromidae + (Oberthueriini + Mirinidae)))]. The remaining bombycoids are grouped, very weakly, as Sphingidae + (Bombycinae + Saturniidae). All multiply‐sampled families are strongly recovered, in both outgroups and ingroups, except that Bombycidae sensu Minet are rendered decisively polyphyletic. All genes make important contributions to the combined data results, and there is little strong conflict among genes or between synonymous and nonsynonymous change, although two instances of inter‐gene conflict were notable, one in Lasiocampidae and one in Mimallonidae. Overall, about 75% of nodes are strongly supported (i.e. bootstrap value ≥80%). Superfamilies are recovered, but not always strongly, whereas relationships among superfamilies are recovered only weakly and inconsistently; even within the reasonably well‐sampled Bombycoidea sensu stricto, a (to us) surprising number of interfamily relationships remain uncertain. Thus, it seems clear that substantially more genes, plus additional taxon sampling in most superfamilies, will be required to resolve macrolepidopteran phylogeny.