Polymorphic Characters Research Articles

Accuracy of Phylogenetic Analysis Including and Excluding Polymorphic Characters

Accuracy of Phylogenetic Analysis Including and Excluding Polymorphic Characters

DNA Amplification Fingerprinting Identifies Closely Related Chrysanthemum Cultivars

DNA amplification fingerprinting (DAF) was used to study genetic relationships between closely related chrysanthemum cultivars (Dendranthema grandiflora Tzvelev.). Twenty-one cultivars were examined that belonged to the Anne, Blush, Boaldi, Charm, Davis, and Pomona series (families). The genetic variability of cultivars within and between series was evaluated using eleven arbitrary octamer primers. A few polymorphic characters uniquely identified closely related cultivars within each of the series. In contrast, many DNA polymorphisms were observed between members of the different series. Phenetic patterns were established by unweighted pair group cluster analysis using arithmetic means (UPGMA) and principal coordinate analysis (PCO). The average distance between series was 10-fold greater than between cultivars within a series. DNA from all cultivars belonging to a series were also bulked to generate profiles containing unique amplified products for each series. Cluster analysis and PCO of bulked DNA clearly grouped Charm and Pomona together. However, series grouping did not correspond to morphology of inflorescence types. The results demonstrate the utility of the DAF technique in distinguishing clonal materials and its potential use for patent protection, phylogenetic studies, and for identifying useful markers in breeding applications.

METHODS FOR FASTER PARSIMONY ANALYSIS

Abstract — Several algorithms to speed up branch swapping searches for most parsimonious trees are described. The method for indirect tree length calculation when moving a clipped clade, based on final states for the divided tree, is expanded to take into account polymorphic characters, and to include the possibility of rejecting several locations as suboptimal by checking just one node. Three different algorithms for faster estimation of final state assignments for the divided tree based on calculations for the whole tree are presented. The first of these is approximate; it uses information from the final state sets for the whole tree. The second is exact, but it is slower than the first, and requires more memory; it is based on the union of the state sets of the descendants for each node. The third is also exact; it requires more memory and programming effort than the other two but it is faster, it is based on final and preliminary state sets for the whole tree (“incremental two‐pass optimization”). Efficient ways to derive state assignments for collapsing trees, based on final states for the divided tree, are described. The recently proposed method of “incremental optimization” is discussed. It is likely that searches using that method will be no faster than searches using indirect calculation as originally described, and will be quite slower than the modified indirect calculation described here. Searches using that method will probably be significantly slowed down when zero‐length branches are to be collapsed, since shortcuts for faster collapsing are not directly applicable.

METHODS FOR FASTER PARSIMONY ANALYSIS

Several algorithms to speed up branch swapping searches for most parsimonious trees are described. The method for indirect tree length calculation when moving a clipped clade, based on final states for the divided tree, is expanded to take into account polymorphic characters, and to include the possibility of rejecting several locations as suboptimal by checking just one node. Three different algorithms for faster estimation of final state assignments for the divided tree based on calculations for the whole tree are presented. The first of these is approximate; it uses information from the final state sets for the whole tree. The second is exact, but it is slower than the first, and requires more memory; it is based on the union of the state sets of the descendants for each node. The third is also exact; it requires more memory and programming effort than the other two but it is faster, it is based on final and preliminary state sets for the whole tree (“incremental two-pass optimization”). Efficient ways to derive state assignments for collapsing trees, based on final states for the divided tree, are described. The recently proposed method of “incremental optimization” is discussed. It is likely that searches using that method will be no faster than searches using indirect calculation as originally described, and will be quite slower than the modified indirect calculation described here. Searches using that method will probably be significantly slowed down when zero-length branches are to be collapsed, since shortcuts for faster collapsing are not directly applicable.

Polymorphic Characters in Phylogenetic Systematics

?The use of discrete, intraspecifkally variable characters in parsimony analysis is re? viewed. Seven data sets (two from morphology and five from allozymes) were analyzed to (1) compare different methods for treating polymorphic characters, (2) test for phylogenetic infor? mation in polymorphic characters, and (3) determine if there is a relationship between homoplasy and intraspecific variability. The performance of eight methods was compared using five criteria (number of characters treated as informative, number of shortest trees, phylogenetic signal, num? ber of nodes supported by bootstrapping, and sensitivity to reduced sample size). Approaches that incorporate explicit frequency information perform best overall for all the criteria, although the majority'' method ties for best for the bootstrapping criterion. Levels of phylogenetic infor? mation in the polymorphic characters differed greatly among data sets and methods. Polymorphic characters in most data sets contained significant phylogenetic structure using most methods, but only one, the frequency method, extracted significant signal from the polymorphic characters in all seven data sets. Fixed characters appear to contain more signal than polymorphic characters, and homoplasy is significantly and positively correlated with intraspecific variability. This study supports the traditional view that polymorphic characters are less reliable in inferring phylogeny but does not necessarily support their exclusion. Systematists working with morphological data often do not report intraspecific variation, the frequencies of different traits, or how polymorphic characters are screened and analyzed; this situation should change. [Polymorphic characters; char? acter coding; character selection; character weighting; homoplasy; allozymes; morphology] Polymorphism, used herein as discrete variation within species that is indepen? dent of ontogenetic and sexual variation, is a ubiquitous problem in phylogenetic anal? ysis. If characters evolve, they must vary within species, at least at some point in their history. Yet, there is a long tradition in systematics of excluding characters in which polymorphism is observed. This practice is evident from the scarcity of phylogenetic studies that report intraspe? cific variation but is difficult to document explicitly because systematists seldom mention the characters that are excluded, rarely give explicit criteria for discarding nonfixed characters, and justify this exclu? sion even less frequently. Presumably, the basis for excluding polymorphic characters is that they are less reliable in phylogenetic inference (e.g., Darwin, 1859; Simpson, 1961; Farris, 1966; Kluge and Farris, 1969; Mayr, 1969) and have traditionally been difficult to deal with analytically (e.g., Wi1 Present address: Section of Amphibians and Rep? tiles, Carnegie Museum of Natural History, Pitts? burgh, Pennsylvania 15213-4080, USA. E-mail: wiens@clpgh.org. ley, 1981). Despite the general stigma as? sociated with polymorphic characters, a number of methods have been developed for their treatment (mostly in the context of analysis of allozyme data), and the rel? ative merits of these methods have been deba ed vigorously (e.g., Farris, 1981; Mickevich and Mitter, 1981, 1983; Buth, 1984; Swofford and Berlocher, 1987; Crother, 1990; Campbell and Frost, 1993; Mabee and Humphries, 1993; Murphy, 1993). Few studies have used analyses of real data sets to examine the properties of polymorphic characters and to compare the different methods for using them (Mickevich and Mitter, 1981; Campbell and Frost, 1993). In this paper, I review the problem of using discrete, intraspecifically variable characters in parsimony analysis. Specifi? cally, I address three questions: (1) What is the best method for phylogenetic analysis of polymorphic characters? (2) Do poly? morphic characters contain useful phylo? genetic information? (3) Is there a relation? ship between levels of intraspecific variability and homoplasy in systematic characters? These questions are addressed

A population-phenetic analysis of morphological polymorphism in Polystoma integerrimum (Monogenea)

The analysis of population phenetics to study some of the polymorphic characters in Polystoma integerrimum (Froelich, 1791) from two populations in the Moscow and Novgorod regions, Russia, revealed discrete variations of these characters, defined as phenes, which are discrete, usually alternative, simple features reflecting the peculiarities of a given genotype. The studies demonstrate that the frequencies of phenes B1, B2, and B3, characterized by peculiarities of the serrations on the lower basal part of the marginal hooks, define the differences in genetic structure of the populations studied. Besides these structural differences, the two populations of Polystoma differ in intrapopulational phenetic diversity, whose index was higher in the Novgorod population. It is suggested that variations in the number of chitinous hooks of the copulatory organ i.e., 5, 6, 7, 9, and 10 hooks, characterize the complex of East-European populations of P. integerrimum.

Estimating multipoint recombination fractions.

The likelihood in linkage investigations can be expressed as a polynomial in the relevant recombination fractions. With polymorphic characters, this can be reduced to a product of separate factors for female and male recombinations, with only mild loss of information. With three generation data the polynomials take a specially simple form. Algorithms are given for finding maximum likelihood estimates and their standard errors.

Genetic diversity and population structure of Trypanosoma brucei: clonality versus sexuality

Genomic fingerprinting by arbitrarily primed PCR was used to analyze the genetic variability among 59 Trypanosoma brucei stocks representing the three T. brucei subspecies isolated from various hosts and different countries in Africa. 14 oligonucleotide primers revealed 355 polymorphic binary characters which were used for phenetic and phylogenetic analysis and to perform recombination tests exploring the linkage disequilibrium in the sample. These was good concordance between arbitrarily primed PCR polymorphisms and isoenzyme data previously collected for many of the same strains [1]. However, the arbitrarily primed PCR typing was more discerning than multilocus enzyme electrophoresis typing. Phenetic and phylogenetic analysis using arbitrarily primed PCR markers did not confirm T. brucei brucei and T. brucei rhodesiense as separate subspecies, but T. brucei gambiense group I was monophyletic, confirming this group as suitable for the subspecies status. With this exception, there were no clear lineages among the sample, other than clustering of East African stocks and clustering of West African stocks. Some features of the phylogenetic analysis suggested that the population structure was not strictly clonal though recombination tests showed linkage disequilibrium, even in the absence of repeated genotypes. While genotypes appear stable enough for tracking in applied studies, sexuality will impact at the evolutionary time scale, and may be more frequent under some ecological conditions. The arbitrarily primed PCR approach should be an effective and simple approach to follow epidemics and to quantify the role of sexuality in T. brucei populations.

Coding Polymorphic Data: Examples from Allozymes and Ontogeny

Limitations for using polymorphic characters in phylogenetic analysis include the lack of computer algorithms that allow input of complex branched or reticulate character state trees and the inability to use polymorphisms as data in tree building and character optimization. The step matrix option in PAUP version 3.0 and MacClade versions 2.1 and 3.0 provides a solution to these problems, allowing all homology information among character states to be utilized while retaining a biologically realistic definition of characters. For genetic data, this means that the locus can be coded as the character and allelic combinations can be coded as the character states. For ontogenetic data, this means that the entire ontogenetic sequence can be coded as the character and combinations of observed conditions within ontogenies can be coded as the character states. The unity of the locus or character ontogeny is preserved, and homology information from shared electrophoretic or ontogenetic conditions is not lost. Attention has not been called to the loss of homology information that accompanies coding the locus or an entire ontogeny as the character, possibly because of the lack of a coding option through which these data could be retained. The step matrix option allows any and all assumptions of transformation (order) among character states while retaining the unity of the locus or a whole ontogeny as the character and can be utilized for coding these and other polymorphic characters for phy? logenetic analysis. (Polymorphic; allozyme; ontogeny; character; order; coding; homology; step matrix.)

POLYMORPHIC TAXA, MISSING VALUES AND CLADISTIC ANALYSIS.

Missing values have been used in cladistic analyses when data are unavailable, inapplicable or sometimes when character states are variable within terminal taxa. The practice of scoring taxa as having "missing values" for polymorphic characters introduces errors into the calculation of cladogram lengths and consistency indices because some character change is hidden within terminals. Because these hidden character steps are not counted, the set of most parsimonious cladograms may differ from those that would be found if polymorphic taxa had been broken into monomorphic subunits. In some cases, the trees found when polymorphisms are scored as missing values may not include any of the most parsimonious trees found when the data are scored properly. Additionally, in some cases, polymorphic taxa may be found to be polyphyletic when broken into monomorphic subunits; this is undetected when polymorphisms are treated as missing. Because of these problems, terminal units in cladistic analysis should be based on unique, fixed combinations of characters. Polymorphic taxa should be subdivided into subunits that are monomorphic for each character used in the analysis. Disregarding errors in topology, the additional hidden steps in a cladogram in which polymorphisms are scored as missing can be calculated by a simple formula, based on the observation that if it is assumed that polymorphic terminals include all combinations of character states, 2p - 1 additional steps are required for each taxon in which p polymorphic binary characters are scored as missing values. Thus, when several polymorphisms are scored as missing in the same taxon, very large errors can be introduced into the calculation of tree length.

Differential production of juvenile hormone and its desoxy precursor by corpora allata of honeybees during a critical period of caste development

In social insects with pronounced caste polymorphism, the caste-inducing external signals are generally transformed into differences in juvenile hormone titer which in turn regulate the expression of polymorphic characters [1]. In the honeybee, the critical period for caste differentiation was found to coincide with the phase of differential feeding of future queens and workers by nurse bees [2]. During the feeding phase of the last (fifth) larval instar, the juvenile hormone titer in future queens is considerably higher than in worker larvae [3, 4].By means of a radiochemical in-vitro assay [5] we could show that an elevated juvenile hormone synthesis in the corpora allata of queen larvae is the prime regulating element for the caste-specific juvenile hormone titer [6]. Since release rates of juvenile hormone were found to be strictly dependent on hormone production [6], potential differences in hormone storage could be excluded as an explanation for the observed phenomenon. At the same time, the intraglandular contents of juvenile hormone III and its immediate desoxy precursor methyl 3,7,11-trimethyldodeca2(E),6(E),10-trienoate (methyl farnesenoate; often termed methyl farnesoate) were found to be correlated in queens but not in workers [6], indicating caste-specific differences in the biosynthetic pathway of juvenile hormone. Based on these results, two hypotheses for the generation of caste differences in juvenile hormone titer were formulated: an enhanced synthetic capacity resulting from an enlargement of the corpora allata in queen larvae, or rate limitations in the terminal steps of juvenile hormone biosynthesis in worker larvae. The present study attempts to answer these questions.

Revision of the dolichoderine ant genus Turneria (Hymenoptera: Formicidae)

Abstract. The Australasian ant genus Turneria is revised. T.bidentata Forel, T.dahlii Forel and T.pacifica Mann are redescribed and a lectotype designated for T.bidentata. T.frenchi Forel is transferred to Stigmacros (comb.n.), and T.butteli Forel is transferred to Iridomyrmex (comb.n.). Three new species, T.arbusta, T.collina and T.postomma, are described from Papua New Guinea. Males of the genus are described for the first time. A key to the workers of recognized species and a distribution map are provided. The group is analysed cladistically and the resulting species relationships are discussed, along with a comment on the use of polymorphic characters.

Protein polymorphism in sheep pedigree testing

Four polymorphic proteins (transferrin, serum arylesterase, hemoglobin and a red-blood-cell lysate protein) were used as genetic markers in a sheep parentage test. It was found that errors in parentage records occurred in a minimum (9.2%) of the progeny. The efficacy of protein genetic markers in solving questionable parentage cases was estimated to be 67.2%. Among all cases, 58.3% were solved on the basis of genetic incompatibility involving transferrin alone. The results of this study demonstrate that the occurrence of errors in pedigrees can be identified by the use of protein polymorphic characters as genetic markers.

Nutritional variation in Escherichia coli.

Nutritional tests were carried out on 62 strains of Escherichia coli as part of a study on the genetic basis of natural nutritional variation. The ability of these strains to utilize 84 compounds as carbon, nitrogen and carbon plus nitrogen sources was tested using an auxanographic method. The tests revealed polymorphic characters which are suitable for genetic analysis. Very few of these strains grew on the amino acids classified as 'essential' for humans.

Shell polymorphism in a southern peripheral population of Cepaea nemoralis (L.) (Pulmonata: Helicidae) in Spain

Populations of the land snail Cepaea nemoralis have been investigated at the southern limits of its range in Spain, the Upper Tajo region, in order to analyse the distribution of the species and the variation of polymorphism in relation to environmental conditions. For this purpose two natural subareas, which differ in topography, soil nature, climate and vegetation have been considered. Cepaea nemoralis is confined to the river banks of the area; it is found in open and shaded biotopes of subarea 1 where it is relatively common, and it is almost restricted to shaded biotopes of subarea 2 where it becomes progressively rarer towards the south. Relative abundance of the species may be related to the amount of calcareous soils and climate, the restriction in its southern distribution being probably the result of extreme solar radiation, high temperature and low humidity. The two subareas differ in the frequency of the main polymorphic characters. These differences may be related to the kind of biotope. Subarea 1 richer in more open and exposed biotopes have higher frequencies of yellow, 00000, 00300, and unfused bands, whereas the restriction to poplar groves because of the lack of suitable exposed biotopes in subarea 2 may account for the higher proportion of pink five-bandeds with the bands fused together. This kind of variation with biotope is consistent with an explanation in terms of differences in the temperature absorbance of different morphs and a metabolic response to differences in temperature amplitude of the biotopes. Other characters (lip colour, punctate bands, hyalozonate bands, etc.) are not polymorphic in this region, thus, suggesting that at the periphery environmental conditions are important not only in determining the distribution of the species but exerting a marked effect on the genetic structure of the populations.

Genetic polymorphism of serum proteins and levels of immunoglobulin and complement components in high caste community (Brahmins) of Madhya Pradesh, India.

Quantitation of C3 and C3 proactivator in a healthy Indian population shows lower levels than in European populations, whereas the levels of all immunoglobulins except IgA are elevated. It is suggested that for the Indian subcontinent the normal IgE level should be taken as 400–500 iu/ml, a figure considerably higher than that in Europe. To assess the possibility of a genetic element in the regional serum protein variation, the association of the immunoglobulin and complement levels with several serum polymorphic characters is examined.

Unusual Distribution of Red Cell Acid Phosphatase among Aborigines of Australia

THE Australian Aborigines are an interesting population for the study of human variability due to inherited characteristics. The first study of their blood groups was published in 1922 (ref. 1) and many extensive surveys have since been undertaken. More recently discovered polymorphic characters, including the serum haptoglobins, transferrins, gamma globulins and group specific types, have also been investigated, and the results have been reviewed2–4. There is, however, no published information about the distribution of red cell acid phosphatase types among the aborigines and the study reported here was undertaken primarily to provide the information.

Glycosyl transferases in mammalian gastric mucosal linings

This chapter discusses the molecular basis of antigenic specificity in the ABO, H, and Lewis blood-group systems. The classical ABO blood group system provided the first examples of single human polymorphic characters that were not associated with inherited diseases, and the understanding of the serological relationships in this system laid the basis for the safe transfusion of blood from one individual to another. The antigenic structures classified within the ABO blood-group system are known to arise through the expression of genes encoding glycosyltransferase enzymes responsible for the terminal glycosylation of carbohydrate chains in glycoproteins, glycolipids and free oligosaccharides. The ABO classification is based on the presence or absence of two antigens, A and B, on the erythrocyte surface and two antibodies anti-A and anti-B which always occur in the plasma when the corresponding antigen is missing. It is the presence of these naturally occurring antibodies that makes knowledge of the ABO groups of crucial importance in blood transfusion.

Polymorphic characters of Tilapia zilii (Gervais)

Polymorphic characters of Tilapia zilii (Gervais)

THE INHERITANCE OF POLYMORPHIC SHELL CHARACTERS IN PARTULA (GASTROPODA)

THE INHERITANCE OF POLYMORPHIC SHELL CHARACTERS IN PARTULA (GASTROPODA)