Chloroplast pigments and algal systematics

The chloroplast pigments of one typical representative (Pleurochloris magna) and two potential members (clone BSG Sticho and an isolate called Tunis) of the new class Eustigmatophyceae have been examined by modern methods including mass spectrometry. The three cultures all exhibited the same chloroplast pigments: Chlorophyll a, but no b or c, δ-carotene (I), canthaxanthin (II), violaxanthin (IIIa), and esterified vaucheriaxanthin (IVb) plus some free vaucheriaxanthin (IVa). Furanoid rearrangement of the epoxidic carotenoids complicated the analysis. The unique pigment complement hereby indicated for Eustigmatophyceae is clearly different from the pigment distribution patterns reported for Chlorophyceae and Xanthophyceae.     

Chloroplast DNA variation in Chlamydomonas and its potential application to the systematics of this genus

We have estimated the extent of chloroplast DNA (cpDNA) variation in three species of green algae belonging to the genus Chlamydomonas to determine if this variation could be used for taxonomic studies. The overall arrangement of sequences in the chloroplast genome of Chlamydomonas eugametos was compared with that of the closely related C. moewusii and that of the more distantly related C. reinhardtii. The results show that the chloroplast genomes of C. eugametos and C. moewusii are essentially co-linear and are highly homologous in sequence while those of C. eugametos and C. reinhardtii have been extensively rearranged and share a relatively low overall sequence homology. This wide range of chloroplast genome organization suggests that the analysis of cp-DNA variation will be useful for the classification of algae belonging to the Chlamydomonas genus.     

Platyrrhine systematics: A simultaneous analysis of molecular and morphological data

Platyrrhine phylogeny has been investigated repeatedly with morphological characters and DNA nuclear gene sequences, with partially inconsistent results. Given the finding in the past decade that the mitochondrial genome is a potentially valuable source of phylogenetic information, we gathered DNA sequence data of a fragment of the 16S and the entire 12S mitochondrial genes. The objectives were to generate a cladistic phylogeny based on these data and to combine them in a simultaneous analysis with morphological characters and preexisting nuclear DNA sequences. Mitochondrial data analyzed on its own yielded a cladogram that was different from those generated with other data sets. The simultaneous analysis of mitochondrial, nuclear, and morphological data yielded a tree most congruent with that generated with nuclear data and to a lesser degree with the morphological one. It depicted a basal dichotomy that led to two major clades: one of them comprised [Atelinae (Callicebus + Pitheciini)] and the other major clade comprised [Aotus ((Cebus, Saimiri) (Callitrichinae))]. The weakest point of the phylogeny was the position of Aotus as basal within their clade as opposed to more closely linked with either the callitrichines or Cebus-Saimiri. Relationships within callitrichines and atelines were unstable as well. The simultaneous phylogenetic analysis of all data sets revealed congruent signal in all of them that was partially obscured in the separate analyses. Am J Phys Anthropol 106:261–281, 1998. © 1998 Wiley-Liss, Inc.     

Gelechioidea (Insecta: Lepidoptera) systematics: a reexamination using combined morphology and mitochondrial DNA data

Phylogenies of Gelechioidea (Insecta: Lepidoptera) historically have been in disagreement and definitions vary at the family and subfamily levels. Addition of new taxa or new characters drastically changes relationships indicating that current phylogenetic schemes require more investigation. This study is the first phylogenetic analysis of Gelechioidea to include molecular data. Here we present a combined analysis using Maximum Parsimony to investigate sister-group relationships within Gelechioidea. The addition of Cytochrome oxidase I and II to revised published morphological matrices gives 453 parsimony informative characters for the 42 taxa for which we have sequence data. The combined analysis resulted in two trees with mostly novel sister-group relationships. These results challenge current concepts of Gelechioidea, suggesting that traditional morphological characters that have united taxa may not be homologous structures and are in need of further investigation. A combination of morphological data with new molecular data will be the most robust method of study for Gelechioidea phylogenetics.     

Chloroplast DNA microsatellite analysis supports a polyphyletic origin for barley

Five barley chloroplast DNA microsatellites (cpSSRs) were used to study genetic relationships among a set of 186 barley accessions—34 Hordeum vulgare ssp. spontaneum (HS accessions) from Morocco, Ethiopia, Cyprus, Crete, Libya, Iraq, Iran, Turkey, Afghanistan and Israel, 122 H. vulgare ssp. vulgare landraces (HV landraces) from Spain, Bolivia (old Spanish introductions), Morocco, Libya and Ethiopia and 20 modern European spring barleys (HV cultivars). All loci were polymorphic in the material studied, with the number of alleles per locus ranging from two to three. Fifteen multi-locus haplotypes were observed, 11 in HS accessions and seven in HV landraces and cultivars. Of the seven haplotypes found in the HV lines, three were shared with the HS accessions, and four were unique. Cluster analysis revealed two main groups, one consisting of HS accessions from Ethiopia and the HV landraces from Spain, Bolivia (old Spanish), Morocco and Ethiopia, whereas the other larger group contained all of the other accessions studied. Based on these grouping and the existence of haplotypes found in the HV landraces and cultivars but not in the HS wild barley, a polyphyletic origin is proposed for barley, with further centres of origin in Ethiopia and the Western Mediterranean.     

Evaluation of four methods of DNA distribution data analysis based on bromodeoxyuridine/DNA bivariate data

Four published methods of DNA-content histogram analysis (those of Fried, Dean and Jett, simplified Dean, and Fox) were compared using a double labeling of different cell populations. Partially synchronized and asynchronous cell populations were incubated with bromodeoxyuridine (BrdUrd) and then stained with an anti-BrdUrd monoclonal antibody and propidium iodide (PI). The fractions of cells in the G1, S, and G2 + M phases were calculated by each method and compared with those derived from G1, S, and G2 + M areas plotted on BrdUrd/DNA bivariate histograms, taken as the "true" values. This procedure enabled an optimal choice of method for a given cell population.     

A comparison of cluster analysis methods using DNA methylation data

MOTIVATION: Aberrant DNA methylation is common in cancer. DNA methylation profiles differ between tumor types and subtypes and provide a powerful diagnostic tool for identifying clusters of samples and/or genes. DNA methylation data obtained with the quantitative, highly sensitive MethyLight technology is not normally distributed; it frequently contains an excess of zeros. Established tools to analyze this type of data do not exist. Here, we evaluate a variety of methods for cluster analysis to determine which is most reliable. RESULTS: We introduce a Bernoulli-lognormal mixture model for clustering DNA methylation data obtained using MethyLight. We model the outcomes using a two-part distribution having discrete and continuous components. It is compared with standard cluster analysis approaches for continuous data and for discrete data. In a simulation study, we find that the two-part model has the lowest classification error rate for mixture outcome data compared with other approaches. The methods are illustrated using DNA methylation data from a study of lung cancer cell lines. Compared with competing hierarchical clustering methods, the mixture model approaches have the lowest cross-validation error for detecting lung cancer subtype (non-small versus small cell). The Bernoulli-lognormal mixture assigns observations to subgroups with the lowest uncertainty. AVAILABILITY: Software is available upon request from the authors. SUPPLEMENTARY INFORMATION: http://www-rcf.usc.edu/~kims/SupplementaryInfo.html     

Chloroplast DNA restriction site data support a narrowed interpretation ofEupatorium (Asteraceae)

Chloroplast DNA (cpDNA) restriction site analysis was used to assess relationships among samples of Eupatorieae from eastern North America. A total of 270 cpDNA variants was recorded from 35 species using 13 restriction enzymes. Phylogenetic analysis usingGalinsoga, Flaveria, andHelianthinae as outgroups indicated that samples ofAgeratina, Hofmeisteria, Mikania, andStevia, each of which have relatively high base chromosome numbers, formed an unresolved basal polytomy. The remaining samples examined formed a well-supported clade, within which there was a split betweenBrickellia, which hasx = 9, and a number of genera withx = 10. Within thex = 10 clade, there was an unresolved trichotomy, with one group ofAgeratum, Conoclinium, Fleischmannia, andCritonia, a second ofLiatris andTrilisa, and a third ofEupatorium s.s. Within theEupatorium s.s. clade there were three further clades, withE. sect.Verticillata diverging first, and a subsequent split between species originating from North America and those from Asia. The cpDNA restriction site data provided support for a relatively narrow interpretation ofEupatorium, and indicated that a high chromosome base number is plesiomorphic for Eupatorieae.     

Chloroplast DNA variation and parentage analysis in 55 apples

The chloroplastic atpB-rbcL spacer and the first 53 codons of the rbcL coding sequence was sequenced for 40 apple cultivars and 15 wild species. This chloroplast DNA region is 904 base pairs long, and only five mutations sites were found among the tested samples. Although the cpDNA variation was low, some parentages are proposed based on the maternal inheritance of plastid DNA: the male and female parents are specified, or else suggested, for Worcester, Discovery, Starking, Starkrimson, Kidd's Orange Red, Priscilla, and Gloster, as well as for the putative wild origin for Malus x domestica.     

Dynamic metabolomic data analysis: a tutorial review

In metabolomics, time-resolved, dynamic or temporal data is more and more collected. The number of methods to analyze such data, however, is very limited and in most cases the dynamic nature of the data is not even taken into account. This paper reviews current methods in use for analyzing dynamic metabolomic data. Moreover, some methods from other fields of science that may be of use to analyze such dynamic metabolomics data are described in some detail. The methods are put in a general framework after providing a formal definition on what constitutes a ‘dynamic’ method. Some of the methods are illustrated with real-life metabolomics examples.     

An analysis of macaque systematics using gene frequency data

Macaque gene frequencies for seven polymorphic protein systems are employed to generate dendrograms via two algorithms. The frequency data employed are drawn from 14 populations of macaques representing nine species. The two algorithms are the unweighted pair group method and an iterative program based on the additive hypothesis. The topologies generated by the two approaches are quite similar. The one major difference, involving M. fuscata, is investigated in detail.As measured by our index of dissimilarity (ID) conspecific populations of M. nemestrina, M. mulatta and M. fascicularis are closely related. Often the ID values separating conspecific groups are in agreement with expectations based on geographic considerations. Interspecific comparisons involving M. mulatta and M. fascicularis also exhibit clinal variation.M. cyclopis and M. fuscata show a particularly strong relationship to M. mulatta. This cluster of three species is closely related to M. fascicularis. M. speciosa, on the other hand, appears to be the most divergent of the species analyzed. The results are considered in light of previous thoughts about macaque systematics based on morphological characteristics.     

Chloroplast biosystematics: chloroplast DNA as a molecular probe

The classification of plants has traditionally been dependent upon the comparative analysis of morphological and biochemical data. In this paper the use of molecular probe analysis of chloroplast DNA (ctDNA) is used to expand the data base used in taxonomic studies. Chloroplast DNA size, homogeneity, the global arrangement of ctDNA structure, gene content, gene cluster array and gene sequence determination are discussed as useful criteria in the analysis of phylogenetic relationships.     

Chloroplast DNA variation and evolution in pisum: patterns of change and phylogenetic analysis

Variation in 30 chloroplast DNAs, representing 22 wild and cultivated accessions in the genus Pisum, was analyzed by comparing fragment patterns produced by 16 restriction endonucleases. Three types of mutations were detected. First, an inversion of between 2.2 kilobase pairs (kb) and 5.2 kb distinguished a population of P. humile from all other Pisum accessions examined. Second, deletions and insertions of between 50 and 1200 base pairs produced small restriction fragment length variations in four regions of the 120-kb chloroplast genome. Two of these regions—one of which is located within the sequence that is inverted in P. humile—showed a high degree of size polymorphism, to the extent that size differences were detected between individuals from the same accession. Finally, a total of only 11 restriction site mutations were detected among the 165 restriction sites sampled in the 30 DNAs. Based on these results and previous data, we conclude that the chloroplast genome is evolving very slowly relative to nuclear and mitochondrial DNAs. The Pisum chloroplast DNA restriction site mutations define two major lineages: One includes all tested accessions of P. fulvum, which is known to be cytogenetically quite distinct from all other Pisum taxa. The second includes 12 of 13 cultivated lines of the garden pea (P. sativum) and a wild population of P. humile from northern Israel. These observations strongly reinforce an earlier conclusion that the cultivated pea was domesticated primarily from northern populations of P. humile. A 13th P. sativum cultivar has a chloroplast genome that is significantly different from those of the aforementioned lines and somewhat more similar to those of P. elatius and southern populations of P. humile. This observation indicates that secondary hybridization may have occurred during the domestication of the garden pea.     

Highly repeated DNA analysis and systematics of the Lemuridae,a family of Malagasy prosimians

Hybridization of highly repeated DNA sequences ofEulemur fulvus mayottensis, Lemur catta, andVarecia has been performed on blots of different species of Lemuridae (L. catta, Hapalemur griseus, Varecia variegata variegata, V. v. rubra, E. macaco macaco, E. coronatus, E. mongoz, andE. rubriventer). The probe ofE. fulvus only hybridized with the differentEulemur species, whereas that ofVarecia hybridized with the two subspecies ofVarecia and that ofL. catta with bothL. catta andHapalemur. These results were used to confirm the classification ofVarecia in a separate genus and to review the separation of theL. catta/Hapalemur group from the other species ofEulemur. Comparison of the migration patterns from DNA fragments of these different species has been used to propose a cladogram of the differentEulemur species.     

Comparing analysis methods for mutation-accumulation data: a simulation study

We simulated single-generation data for a fitness trait in mutation-accumulation (MA) experiments, and we compared three methods of analysis. Bateman-Mukai (BM) and maximum likelihood (ML) need information on both the MA lines and control lines, while minimum distance (MD) can be applied with or without the control. Both MD and ML assume gamma-distributed mutational effects. ML estimates of the rate of deleterious mutation had larger mean square error (MSE) than MD or BM had due to large outliers. MD estimates obtained by ignoring the mean decline observed from comparison to a control are often better than those obtained using that information. When effects are simulated using the gamma distribution, reducing the precision with which the trait is assayed increases the probability of obtaining no ML or MD estimates but causes no appreciable increase of the MSE. When the residual errors for the means of the simulated lines are sampled from the empirical distribution in a MA experiment, instead of from a normal one, the MSEs of BM, ML, and MD are practically unaffected. When the simulated gamma distribution accounts for a high rate of mild deleterious mutation, BM detects only approximately 30% of the true deleterious mutation rate, while MD or ML detects substantially larger fractions. To test the robustness of the methods, we also added a high rate of common contaminant mutations with constant mild deleterious effect to a low rate of mutations with gamma-distributed deleterious effects and moderate average. In that case, BM detects roughly the same fraction as before, regardless of the precision of the assay, while ML fails to provide estimates. However, MD estimates are obtained by ignoring the control information, detecting approximately 70% of the total mutation rate when the mean of the lines is assayed with good precision, but only 15% for low-precision assays. Contaminant mutations with only tiny deleterious effects could not be detected with acceptable accuracy by any of the above methods.     

Phylogenetic analysis and comparative data: a test and review of evidence

The question is often raised whether it is statistically necessary to control for phylogenetic associations in comparative studies. To investigate this question, we explore the use of a measure of phylogenetic correlation, lambda, introduced by Pagel (1999), that normally varies between 0 (phylogenetic independence) and 1 (species' traits covary in direct proportion to their shared evolutionary history). Simulations show lambda to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error. Moreover, lambda is robust to incomplete phylogenetic information, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses. To assess whether traits generally show phylogenetic associations, we present a quantitative review of 26 published phylogenetic comparative data sets. The data sets include 103 traits and were chosen from the ecological literature in which debate about the need for phylogenetic correction has been most acute. Eighty-eight percent of data sets contained at least one character that displayed significant phylogenetic dependence, and 60% of characters overall (pooled across studies) showed significant evidence of phylogenetic association. In 16% of tests, phylogenetic correlation could be neither supported nor rejected. However, most of these equivocal results were found in small phylogenies and probably reflect a lack of power. We suggest that the parameter lambda be routinely estimated when analyzing comparative data, since it can also be used simultaneously to adjust the phylogenetic correction in a manner that is optimal for the data set, and we present an example of how this may be done.     

A review of some statistical methods for covariance analysis of categorical data

Three general methods for covariance analysis of categorical data are reviewed and applied to an example from a clinical trial in rheumatoid arthritis. The three methods considered are randomization-model nonparametric procedures, maximum likelihood logistic regression, and weighted least squares analysis of correlated marginal functions. A fourth heuristic approach, the unweighted linear model analysis, is an approximate procedure but it is easy to implement. The assumptions and statistical issues for each method are discussed so as to emphasize philosophical differences between their rationales. Attention is given to computational differences, but it is shown that the methods lead to similar results for analogous problems. It is argued that the essential differences between the methods lie in their underlying assumptions and the generality of the conclusions which may be drawn.     

Embryology and systematics of Euphorbiaceaesens. lat.: a review and perspective

Based on a literature survey, we present a review of the embryology of Euphorbiaceaesensu Webster (with about 8,000 species in five subfamilies), which are one of the largest and most diversified families and have often been considered heterogenous. Nearly 40% of over 110 publications available for the whole family is concerned with a single genusEuphorbia, so that the current level of our knowledge on the embryology of Euphorbiaceae is very poor. Nevertheless we found that, contrary to a conclusion recently published by other authors, available information does not provide evidence to support a monophyly of Euphorbiaceae. Our analysis further suggested that only the following five of over 50 embryological characters of ovules and seeds are likely to be useful for comparison between and within subfamilies: (1) the presence or absence of vascular bundles in the inner integument; (2) whether the inner integument is thick or thin (probably useful only in Phyllanthoideae); (3) whether ovules or seeds are pachychalazal or not; (4) whether seeds are arillate or not; (5) whether an exotegmen is fibrous or not. On the basis of these five characters, a consistency and diversity of individual subfamilies was discussed. The need of further extensive studies on the five characters using herbarium specimens, particularly in genera of Phyllanthoideae, Oldfieldioideae and Acalyphoideae, was also discussed.