Brooks Parsimony Analysis: a valiant failure

A recent comparison of two methods for examining correlated host and parasite phylogenies, namely TreeMap 1.0 and Brooks Parsimony Analysis concluded that the latter method performed better and is to be preferred. Reevaluation of the examples contrived for that study demonstrates that the two methods were only compared on one kind of problem (widespread parasite) for which there is an easy fix for TreeMap 1.0. Other kinds of problems like host‐switching among sister taxa or host‐switching over great distances across a host tree befuddle BPA even as they are readily resolved parsimoniously by TreeMap 1.0. These difficulties, compounded with inaccurate counting of ad hoc hypotheses required by its solutions render BPA unsuitable for comparison of host and parasite phylogenies.     

A priori and a posteriori methods in comparative evolutionary studies of host–parasite associations

Brooks parsimony analysis (BPA) and reconciliation methods in studies of host–parasite associations differ fundamentally, despite using the same null hypothesis. Reconciliation methods may eliminate or modify input data to maximize fit of single parasite clades to a null hypothesis of cospeciation, by invoking different a priori assumptions, including a known host phylogeny. By examining the degree of phylogenetic congruence among multiple parasite clades, using hosts as analogs of taxa but not presuming a host phylogeny or any degree of cospeciation a priori, BPA modifies the null hypothesis of cospeciation if necessary to maintain the integrity of the input data. Two exemplars illustrate critical empirical differences between reconciliation methods and BPA: (1) reconciliation methods rather than BPA may select the incorrect general host cladogram for a set of data from different clades of parasites, (2) BPA rather than reconciliation methods provides the most parsimonious interpretation of all available data, and (3) secondary BPA, proposed in 1990, when applied to data sets in which host‐switching produces hosts with reticulate histories, provides the most parsimonious and biologically realistic interpretations of general host cladograms. The extent to which these general host cladograms, based on cospeciation among different parasite clades inhabiting the same hosts, correspond to host phylogeny can be tested, a posteriori, by comparison with a host phylogeny generated from nonparasite data. These observations lead to the conclusion that BPA and reconciliation methods are designed to implement different research programs based on different epistemologies. BPA is an a posteriori method that is designed to assess the host context of parasite speciation events, whereas reconciliation methods are a priori methods that are designed to fit parasite phylogenies to a host phylogeny. Host‐switching events are essential for explaining complex histories of host–parasite associations. BPA assumes coevolutionary complexity (historical contingency), relying on parsimony as an a posteriori explanatory tool to summarize complex results, whereas reconciliation methods, which embody formalized assumptions of maximum cospeciation, are based on a priori conceptual parsimony. Modifications of basic reconciliation methods, embodied in TreeMap 1.0 and TreeMap 2.02, represent the addition of weighting schemes in which the researcher specifies allowed departures from cospeciation a priori, with the result that TreeMap results more closely agree with BPA results than do reconciled tree analysis results.     

Extending phylogenetic studies of coevolution: secondary Brooks parsimony analysis, parasites, and the Great Apes

Dowling recently compared the empirical properties of Brooks parsimony analysis (BPA) and the leading method for studying phylogenetic aspects of coevolution, reconciled tree analysis (using the computer program TreeMap), based on a series of simulations. Like the majority of authors who have compared BPA with other methods, however, Dowling considered only the form of BPA proposed in 1981 and did not take into account various modifications of the method proposed from 1986 to 2002. This leaves some doubt as to the robustness of his assessments of both the superiority of BPA and its shortcomings. We provide a précis of the principles of contemporary BPA, including ways to implement it algorithmically, using either Wagner algorithm‐based or Hennigian argumentation‐based approaches, followed by an empirical example. Our study supports Dowling's fundamental conclusions about the superiority of primary BPA relative to TreeMap. However, his conclusions about the shortcomings of BPA due to inclusive ORing (i.e., the production of ghost taxa) are incorrect, as secondary BPA eliminates inclusive ORing from the method. Secondary BPA provides a more complete account of the evolutionary associations between the parasite groups and their hosts than does primary BPA, without sacrificing any indirectly generated information about host phylogeny. Secondary BPA of two groups of nematodes inhabiting Great Apes shows that TreeMap analysis underestimated the amount of cospeciation in the evolution of the nematode genus Enterobius.     

Testing the accuracy of TreeMap and Brooks parsimony analyses of coevolutionary patterns using artificial associations

Brooks parsimony analysis and TreeMap are the two most commonly used methods and are tested using artificially evolved host–parasite associations with varying amounts of coevolutionary events occurring between the two “phylogenies.” The purpose is to test the precision with which each method recovers the true coevolutionary history. The reconstructions recovered by each method are compared against the original test case to determine how closely the reconstruction resembles the artificially created coevolutionary history. Brooks parsimony analysis is found to be consistently less prone to gross overestimation of coevolutionary events and misleading results. Brooks parsimony analysis performs better overall because it is more adept at dealing with host-switching events, both between and within lineages leading to widespread parasite taxa, which provides enough evidence for implementing Brooks parsimony analysis instead of TreeMap in coevolutionary studies.     

Marine Area Relationships from Twenty Sponge Phylogenies. A Comparison of Methods and Coding Strategies

Published phylogenies of 20 marine sponge groups are used to build general area cladograms of marine areas of endemism under three different methods for which algorithms adapted for personal computers are available, viz. COMPONENT, BPA and TAS, and two different coding strategies, Assumption 0 (A0) and "no assumption" (NA). The latter is a recently proposed procedure for handling the distributions of widespread taxa by treating these as separate areas of endemism, rather than as suites of smaller constituent areas. The 20 phylogenies contained large numbers of problem data which prevented an exhaustive search for all possible equally "best" general area cladograms. The Nelson consensus trees and their equivalents in parsimony analysis for all six attempts (viz. three different methodologies under two different coding strategies) were compared using their fit with the 20 sponge phylogenies as a measure of quality. Fit was determined using the number of "cospeciations" between a general area cladogram and a taxon area cladogram computed with TreeMap 1.0. No single method or coding strategy yielded a clearly better fit, each cladogram fitting variously better or worse with various phylogenies. In general, fit with NA coding was higher than with A0 coding, but random tree tests failed to generate statistically significant support for the conclusion that NA coding improves fit. Assuming that available sponge phylogenies are representative of marine benthic groups, software and hardware limitations are serious obstacles to a successful development of marine general area cladograms under any method or coding strategy.     

Computational aspects of host-parasite phylogenies

Computational aspects of host-parasite phylogenies form part of a set of general associations between areas and organisms, hosts and parasites, and species and genes. The problem is not new and the commonalities of exploring vicariance biogeography (organisms tracking areas) and host-parasite co-speciation (parasites tracking hosts) have been recognised for some time. Methods for comparing host-parasite phylogenies are now well established and fall within two basic categories defined in terms of the way the data are interpreted in relation to the comparison of host-parasite phylogenies, so-called a posteriori, eg Brooks' Parsimony Analysis (BPA), or a priori, eg reconciled trees and other model-based methods, as implemented in the program TreeMap; the relative merits of the two philosophies inherent in these two approaches remain hotly debated. This paper reviews the computational methods currently available to analyse host-parasite relationships.     

Cophylogenetic relationships between penguins and their chewing lice

It is generally thought that the evolution of obligate parasites should be linked intimately to the evolution of their hosts and that speciation by the hosts should cause speciation of their parasites. The penguins and their chewing lice present a rare opportunity to examine codivergence between a complete host order and its parasitic lice. We estimated a phylogeny for all 15 species of lice parasitising all 17 species of penguins from the third domain of the mitochondrial 12S ribosomal rRNA gene, a portion of the mitochondrial cytochrome oxidase subunit 1 gene and 55 morphological characters. We found no evidence of extensive cospeciation between penguins and their chewing lice using TreeMap 2.02beta. Despite the paucity of cospeciation, there is support for significant congruence between the louse and penguin phylogenies due to possible failure to speciate events (parasites not speciating in response to their hosts speciating).     

Ultrasensitive one-step rapid visual detection of bisphenol A in water samples by label-free aptasensor

A simple, one-step, rapid method to detect bisphenol A (BPA) using a label-free aptasensor is presented. A high selective anti-BPA aptamer was added to gold nanoparticles (GNPs) to prepare the label-free aptasensor for BPA, which maintains good tolerance of GNPs under aqueous conditions with high salt concentrations. With the presence of BPA in the aptasensor system, the GNPs would aggregate by competitive binding of BPA and aptamer. Detection results can be visualized by the aggregation-induced color change of GNPs without the use of any instrumentation. The limit of visual detection (LOD) was found to be 0.1ng/mL by naked-eye observation, which was competitive to some current rapid BPA detection methods, even some instrumental based methods. Besides the obvious advantages, including reduced detection time and operation procedures, the results of this method meet the various detection requirements for BPA and are comparable to the traditional ELISA and instrument-based methods. The proposed one-step, label-free method was successfully used to determine BPA in actual water samples.     

Comparing host and parasite phylogenies: gyrodactylus flatworms jumping from goby to goby

The combination of exceptionally high species diversity, high host specificity, and a complex reproduction system raises many questions about the underlying mechanisms triggering speciation in the flatworm genus Gyrodactylus. The coevolutionary history with their goby hosts was investigated using both topology- and distance-based approaches; phylogenies were constructed of the V4 region of the 18S rRNA and the complete ITS rDNA region for the parasites, and 12S and 16S mtDNA fragments for the hosts. The overall fit between both trees was significant according to the topology-based programs (TreeMap 1.0, 2.0 beta and TreeFitter), but not according to the timed analysis in TreeMap 2.0 beta and the distance-based method (ParaFit). An absolute timing of speciation events in host and parasite ruled out the possibility of synchronous speciation for the gill parasites, favouring the distance-based result. Based on this information together with the biological background of host and parasite, the following TreeMap solution was selected. The group of gill parasites evolved from a host switch from G. arcuatus, parasitizing the three-spined stickleback onto the gobies, followed by several host-switching events among the respective goby hosts. The timing of these events is estimated to date back to the Late Pleistocene, suggesting a role for refugia-mediated mixing of parasite species. In contrast, it is suggested that co-speciation in the fin-parasites resulted in several host-associated species complexes. This illustrates that phylogenetically conserved host-switching mimics the phylogenetic signature of co-speciation, confounding topology-based programs.     

Coevolution between Lamellodiscus (Monogenea: Diplectanidae) and Sparidae (Teleostei): the study of a complex host-parasite system

Abstract.— Host-parasite coevolution was studied between Sparidae (Teleostei) fishes and their parasites of the genus Lamellodiscus (Monogenea, Diplectanidae) in the northwestern Mediterranean Sea. Molecular phylogenies were reconstructed for both groups. The phylogenetic tree of the Sparidae was obtained from previously published 16S mitochondrial DNA (mtDNA) sequences associated with new cytochrome-b mtDNA sequences via a "total evidence" procedure. The phylogeny of Lamellodiscus species was reconstructed from 18S rDNA sequences that we obtained. Host-parasite coevolution was studied through different methods: TreeFitter, TreeMap, and a new method, ParaFit. If the cost of a host switch is not assumed to be high for parasites, all methods agree on the absence of widespread cospeciation processes in this host-parasite system. Host-parasite associations were interpreted to be due more to ecological factors than to coevolutionary processes. Host specificity appeared not to be related to host-parasite cospeciation.     

When simplicity is not parsimonious: a priori and a posteriori methods in historical biogeography

Despite using the same null hypothesis, a priori and a posteriori approaches in historical biogeography differ fundamentally. Methods such as Component Analysis (CA) and Reconciled Tree Analysis (RTA) may eliminate or modify input data in order to maximize fit to the null hypothesis, by invoking assumptions 1 and 2. Methods such as Brooks Parsimony Analysis (BPA) modify the null hypothesis, if necessary, to maintain the integrity of the input data, as required by assumption 0. Two exemplars illustrate critical empirical differences between CA/RTA and BPA: (1) CA rather than BPA may select the incorrect general area cladogram for a set of data (2) BPA, not RTA, provides the most parsimonious interpretation of all available data and (3) secondary BPA, proposed in 1990, applied to data sets for which dispersal producing areas with reticulate histories is most parsimonious, provides biologically realistic interpretations of area cladograms. These observations lead to the conclusion that BPA and CA/RTA are designed to implement different research programmes based on different conceptual frameworks. BPA is designed to assess the biogeographic context of speciation events, whereas CA/RTA are designed to find the best fitting pattern of relationships among areas based on the taxa that inhabit them. Unique distributional elements and reticulate (hybrid) histories of areas are essential for explaining complex histories of speciation. The conceptual framework for BPA, thus, assumes biogeographical complexity, relying on parsimony as an explanatory tool to summarize complex results, whereas CA/RTA assumes biogeographical simplicity, assuming conceptual parsimony a priori .     

Typical versions of learned swamp sparrow song types are more effective signals than are less typical versions

The learned songs of songbirds often cluster into population-wide types. Here, we test the hypothesis that male and female receivers respond differently to songs depending on how typical of those types they are. We used computational methods to cluster a large sample of swamp sparrow (Melospiza georgiana) songs into types and to estimate the degree to which individual song exemplars are typical of these types. We then played exemplars to male and female receivers. Territorial males responded more aggressively and captive females performed more sexual displays in response to songs that are highly typical than to songs that are less typical. Previous studies have demonstrated that songbirds distinguish song types that are typical for their species, or for their population, from those that are not. Our results show that swamp sparrows also discriminate typical from less typical exemplars within learned song-type categories. In addition, our results suggest that more typical versions of song types function better, at least in male–female communication. This finding is consistent with the hypothesis that syllable type typicality serves as a proxy for the assessment of song learning accuracy.     

Bisphenol A: a scientific evaluation

Bisphenol A (BPA) is used in the production of high-volume polycarbonate and epoxy resin compounds found in a number of consumer products, including plastic bottles and the linings of canned goods. As a result of such applications, very small amounts of BPA can migrate into food and drink. In light of reports suggesting that low doses of BPA cause estrogenic effects in laboratory animals, concerns were raised about the safety of these consumer products, particularly plastic bottles used for feeding milk to babies. To evaluate the risk, if any, from BPA, investigations were undertaken to more precisely determine human exposure levels and more carefully study the validity of the low-dose effects reported. On the basis of the most realistic studies of BPA levels in food and drink, as well as in human urine, it has been estimated that human exposures, including those of children, are very low and range from about .001 to .1 mcg/kg body weight (bw)/day. The results of the additional toxicology studies indicated that the low-dose effects could not be consistently replicated. In light of this, a number of governments and agencies brought together independent expert panels to carefully evaluate the toxicologic studies and provide regulatory guidance. These panels came to a similar conclusion, namely, that low-dose effects have not been demonstrated. They also supported the acceptable daily intake levels previously calculated on the basis of high-dose effects shown in laboratory animals. Comparing these acceptable intakes with the best exposure estimates reveals that human doses of BPA from migration of the compound into food and drink are orders of magnitude lower than acceptable daily intakes. Thus, it is very unlikely that humans, including infants and young children, are at risk from the presence of BPA in consumer products.     

ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes

A new system, ZCURVE 1.0, for finding protein- coding genes in bacterial and archaeal genomes has been proposed. The current algorithm, which is based on the Z curve representation of the DNA sequences, lays stress on the global statistical features of protein-coding genes by taking the frequencies of bases at three codon positions into account. In ZCURVE 1.0, since only 33 parameters are used to characterize the coding sequences, it gives better consideration to both typical and atypical cases, whereas in Markov-model-based methods, e.g. Glimmer 2.02, thousands of parameters are trained, which may result in less adaptability. To compare the performance of the new system with that of Glimmer 2.02, both systems were run, respectively, for 18 genomes not annotated by the Glimmer system. Comparisons were also performed for predicting some function-known genes by both systems. Consequently, the average accuracy of both systems is well matched; however, ZCURVE 1.0 has more accurate gene start prediction, lower additional prediction rate and higher accuracy for the prediction of horizontally transferred genes. It is shown that the joint applications of both systems greatly improve gene-finding results. For a typical genome, e.g. Escherichia coli, the system ZCURVE 1.0 takes approximately 2 min on a Pentium III 866 PC without any human intervention. The system ZCURVE 1.0 is freely available at: http://tubic. tju.edu.cn/Zcurve_B/.     

Rhinoplasty: a simplified, three-stitch, open tip suture technique. Part I: primary rhinoplasty

Tip suture techniques offer a reliable and dramatic method of tip modification without needing to interrupt the alar rim strip or add tip grafts. The present simplified three-stitch technique consists of the following: (1) a strut suture to fix the columella strut between the crura, (2) bilateral domal creation sutures to create tip definition, and (3) a domal equalization suture to narrow and align the domes. If required, columella septal sutures can be added; either a dorsal rotational suture or a transfixion projection suture can be used. This simplified method represents a refinement based on more than 13 years of experience with tip suture techniques. It does not require a complex operative sequence or specialized sutures. Primary indications are moderate tip deformities of inadequate definition and excessive width and certain specific tip deformities, including the parenthesis tip and nostril/tip disproportion. The primary contraindications are for patients with minor tip deformities that are best done through a closed approach and those with severe tip deformities requiring an open structure graft. The technique is simple, efficacious, and easily learned.     

The naringenin-induced proapoptotic effect in breast cancer cell lines holds out against a high bisphenol a background

Fruit and vegetable consumption has generally been associated with the prevention or suppression of cancer. However, food could contain a multitude of chemicals (e.g., bisphenol A; BPA) that could synergize or antagonize the effects of diet-derived compounds. Remarkably, food containers (e.g., water and infant bottles) are the largest source of exposure to BPA for human beings. Here, the effects of the coexposure of naringenin (Nar, 1.0 × 10(-9) M to 1.0 × 10(-4) M) and BPA (1.0 × 10(-5) M) in estrogen-dependent breast cancer cell lines expressing (i.e., MCF-7 and T47D) or not expressing (i.e., MDA-MB-231) estrogen receptor α (ERα) are reported. Although both Nar and BPA bind to ERα, they induce opposite effects on breast cancer cell growth. BPA induces cell proliferation, whereas Nar only decreases the number of ERα-positive cells (i.e., MCF-7 and T47D). Notably, even in the presence of BPA, Nar impairs breast cancer cell proliferation by activating caspase-3. The molecular pathways involved require p38 activation, whereas, the BPA-induced AKT activation is completely prevented by the Nar treatment. As a whole, Nar maintains its proapoptotic effects even in the presence of the food contaminant BPA, thus, enlarging the chemopreventive potential of this flavanone.     

Critique of parsimony analysis of endemicity as a method of historical biogeography

Aim Assess the value of parsimony analysis of endemism as either an a priori (cladistic) and an a posteriori (phylogenetic) method of historical biogeography. Location World‐wide. Methods Parsimony analysis of endemicity (PAE) and Brooks parsimony analysis (BPA). Results Parsimony analysis of endemicity is capable of finding correct and unambiguous area relationships only under scenarios of vicariance in combination with non‐response to vicariance or extinction. An empirical comparison between PAE and BPA, using the poeciliid fish genera Heterandria and Xiphophorus, demonstrates that PAE fails to document much of the historical complexity in this relatively simple system. Main conclusions The a priori assumptions of PAE are far more restrictive than those made by other a priori methods, limiting its utility as a method of cladistic biogeography. The inability of PAE to detect perfect vicariance or biogeographical histories involving dispersal, renders it unsuitable as a method of phylogenetic biogeography.     

Comparative structural analysis of desmoplakin, bullous pemphigoid antigen and plectin: members of a new gene family involved in organization of intermediate filaments.

Desmoplakins (DP) and bullous pemphigoid antigen (BPA) are major plaque components of the desmosome and hemidesmosome, respectively. These cell adhesion structures are both associated intimately with the intermediate filament (IF) network. Structural analyses of DP and BPA sequences have indicated that these molecules are likely to form extended dumbbell-shaped dimers with a central rod and globular end domains. Recent sequence data have indicated that the N-terminal domains of both DP and BPA (like their C-terminal domains) are highly related: the former contain regions of heptad repeats that are predicted to form several alpha-helical bundles. Comparisons of DP and BPA protein sequences with that of plectin (PL), a 466 kDa IF-associated protein, have also revealed large scale homology. Identities between their N-terminal domains are: DP:BPA = 35%, DP:PL = 32%, BPA:PL = 40%, suggesting that BPA is more closely related to PL than DP in this region. In the C-terminal domains, which contain a 38-residue repeating motif, however, DP and PL are closer relatives (identities: DP:BPA = 38%, BPA:PL = 40%, DP:PL = 49%). The central domains of all three proteins have extensive heptad repeat substructure, express the same periodic distribution of charged residues, and are predicted to form two-stranded alpha-helical coiled-coil ropes. These observations suggest that DP, BPA and PL belong to a new gene family encoding proteins involved in IF organization.     

Bisphenol A: an endocrine disruptor with widespread exposure and multiple effects

Bisphenol A (BPA) is one of the highest volume chemicals produced worldwide. This compound is a building block of polycarbonate plastics often used for food and beverage storage, and BPA is also a component of epoxy resins that are used to line food and beverage containers. Studies have shown that BPA can leach from these and other products in contact with food and drink, and as a result, routine ingestion of BPA is presumed. This compound is also found in an enormous number of other products that we come into contact with daily, and therefore it is not surprising that it has been detected in the majority of individuals examined. BPA is a known endocrine disruptor. Although initially considered to be a weak environmental estrogen, more recent studies have demonstrated that BPA may be similar in potency to estradiol in stimulating some cellular responses. Moreover, emerging evidence suggests that BPA may influence multiple endocrine-related pathways. Studies in rodents have identified adverse effects of BPA at levels at or below the current acceptable daily intake level for this compound. The various reported adverse effects of BPA are reviewed, and potential mechanisms of BPA action are discussed. Much more investigation is needed to understand the potential adverse health effects of BPA exposure in humans and to understand the multiple pathways through which it may act. Although many questions remain to be answered, it is becoming increasingly apparent that exposure to BPA is ubiquitous and that the effects of this endocrine disruptor are complex and wide-ranging.     

High-performance liquid chromatographic analysis of bisphenol A and 4-nonylphenol in serum, liver and testis tissues after oral administration to rats and its application to toxicokinetic study

A sensitive and simple method based on solid-phase extraction (SPE) and HPLC with fluorescence detection for the determination of bisphenol A (BPA) and 4-nonylphenol (4-NP) in rat serum, liver and testis tissues has been developed. The chromatographic conditions consisted of a C18 column and mobile phase composition of acetonitrile and water with flow rate of 1.0 ml/min. The fluorescence detection was performed at excitation and emission wavelengths of 227 nm and 313 nm, respectively. Under these conditions, BPA and 4-NP were well separated and showed good linearities in the ranges of 0.01-50.0 microg/ml for BPA and 0.15-150.0 microg/ml for 4-NP with correlation coefficients greater than 0.999. The detection limits of serum and tissue samples were 2.8 ng/ml and 1.4 ng/g for BPA and 5.6 ng/ml and 2.8 ng/g for 4-NP at a signal-to-noise ratio (S/N) of 3. The intra-assay and the inter-assay precisions were better than 11.4%. Recoveries of BPA and 4-NP were 78.6-95.0% and 80.2-93.4%, respectively. The proposed method was applied to a toxicokinetic study of BPA and 4-NP including individual and combined oral administration to rats. The results showed that 4-NP remarkably altered the toxicokinetic parameters of BPA in testis, while parameters of BPA were not obviously altered in serum and liver under the experimental conditions investigated. On the other hand, there was no significant difference in the toxicokinetics of 4-NP when administered with BPA.