P-values for group sequential testing

Group sequential testing procedures are widely employed in long-termclinical trials. We discuss several methods for computing theP-value following a group sequential trial based on differentoutcome-space orderings. We use a criterion defined in thispaper to compare these methods and point out interesting differences.     

Seasonal shifts in genotype frequencies in the invasive cladoceran Daphnia lumholtzi in Lake Texoma,U.S.A.

1. We examined the ecological genetics of the invasive cladoceran Daphnia lumholtzi in a reservoir (Lake Texoma) in the southern USA. This species originates from the Old World subtropics and has spread across North America since the late 1980s after its inadvertent introduction to a reservoir in northeastern Texas. 2. The population genetic structure of D. lumholtzi was examined seasonally on 22 dates over a 3‐year period along a natural temperature and salinity gradient. 3. A two‐allele polymorphism at the phosphoglucose isomerase (PGI) locus was detected, while other loci tested showed no variation. Significant temporal heterogeneity existed in genotype frequencies with a major shift between summer and autumn. 4. Results of a multiple linear regression analysis revealed that a significant amount of variation was explained by day length, temperature and conductivity. Additionally, significant spatial heterogeneity of genotype frequencies between lake stations was observed, but was restricted to the summer. 5. Clonal isolates were used in controlled laboratory temperature and salinity tolerance experiments. Results suggest that salinity and temperature tolerance differed between PGI genotypes. 6. Genotype × environment interactions may play a significant role in the micro‐evolutionary dynamics of this invasive species and may have facilitated its rapid expansion across the North American continent.     

Mitochondrial DNA variable number tandem repeats (VNTRs): utility and problems in molecular ecology

Analysis of mitochondrial (mt)DNA size polymorphism in the form of variable number tandem repeats (mtVNTRs) has become an increasingly popular methodology for addressing questions in molecular ecology. When detected by PCR, mtVNTR analysis can provide a sensitive, rapid, and cost-effective measure of genetic variability that may be exploited in studies of population differentiation and biogeography. Despite the emergence of this approach, there has been little critical evaluation of its success or utility as a practical tool. In this review, we identify problematic methodological, theoretical and interpretive factors that can influence the utility of mtVNTR analysis. The reliability of the procedure is considered in terms of both detection of alleles and scoring of intra-individual allele frequencies. While many of the potential technical problems of the technique do not raise serious practical concerns, this rapid and sensitive methodology is seriously compromised by the difficulty of reliably assessing allele frequencies, of assaying only germline tissue, and in our ignorance of the mechanisms generating mtVNTR diversity. Thus, although there is a considerable potential for mtVNTR pilot studies to assess genetic diversity, the utility of the technique to resolve broader questions in molecular ecology should be treated cautiously until such a time as the system is better understood.     

Transformation in Tetrahymena pyriformis: Description of an Inducible Phenotype*†

SYNOPSIS. Transformation of Tetrahymena pyriformis to a rapid-swimming (presumably dispersal) form can be induced by washing cells and suspending them in distilled H₂O, Dryl's solution or 10 mm Tris. Transformation is possible with high efficiency in mass cultures of axenically grown cells within ～ 5 h at 30 C. The radically different phenotype produced during transformation is characterized by a more elongate body form, increased numbers of somatic basal bodies and cilia, a long caudal cilium and oral membranelles positioned beneath the cell surface. DNA quantities characteristic of G1, S, and G2 cells are found in these transformed ciliates, suggesting that achievement of a particular stage in the DNA-division cycle is not a prerequisite for transformation. Preliminary observations on cells belonging to syngens 2–12 indicate that they also have a capacity to form a caudal cilium, but that the amicronucleate strain GL-C does not. Possible relevance of the transformed phenotype for taxonomy of Tetrahymena is discussed.     

Relationships between rust resistance genes at the M locus in flax

Genes at the M locus in flax ( Linum usitatissimum ) that confer resistance to flax rust ( Melampsora lini ) occur in complex haplotypes containing up to 15 related genes or gene fragments. We have cloned two additional functional resistance genes at this locus, M1 and M3 , by transposon tagging and candidate gene approaches, and investigated the genetic relationships between four genes ( M , M1 , M3 and M4 ) by recombination analysis. M1 and M3 , like M , are members of the nucleotide binding site, leucine-rich repeat (NBS-LRR) family. Comparisons of the predicted M1 and M3 amino acid sequences with M and L6 reveal that: (i) M1 contains four additional LRRs, probably as a result of an unequal crossover event between duplicated regions; (ii) M1 shares large segments of exact identity with M and M3, indicative of intragenic recombination events; and (iii) a large number of amino acid differences are scattered throughout the M, M1 and M3 proteins. Recombination analysis (here and in previous studies) has revealed that M readily recombines with M1 , M3 and M4 , whereas these three genes fail to recombine despite large family sizes (>5800) in two test-cross families, suggesting that they may occupy allelic positions in the gene cluster. Several restriction fragment length polymorphism markers within or near the M locus were mapped with respect to seven crossover events between M and M1 . The results of this and previous studies provide evidence of structural differences between: (i) homoeologous loci in the different genomes of flax; (ii) different haplotypes at the M locus; (iii) different resistance genes in the M group; and (iv) the flanking regions downstream of M locus resistance genes.     

The evolution of Spartina anglica G. E. Hubbard (Gramineae): genetic variation and status of the parental species in Britain

The perennial salt marsh grass Spartina anglica is one of the classic examples of allopolyploid speciation. It originated on the south coast of England at the end of the nineteenth century following chromosome doubling in S. × townsmdii , a hybrid between the native British S. marilima and a species introduced from the United States, S. alterniflora. The nature of the origin of S. anglica is beyond doubt; however, it is not known whether it had a single or multiple origin. In order to address this problem we undertook a survey of the genetic variation in the parental species of S. anglica using isozyme electrophoresis. The results show that S. alterniflora has no detectable variation and that S. maritima has extremely low levels of variation. These results, unfortunately, prevent the question of a single or multiple origin from being answered. Possible reasons for the low levels of variation and its influence on the future of the species are discussed. Another problem concerning the parental species is the rapid decline of S. maritima in Britain. It is often assumed that the major factor in this regression is the invasion of its habitats by S. anglica. We have examined the status of S. marilima throughout its range in Britain and have found that S. anglica rarely co-occurs with S. maritima. We propose that the decline of S. maritima is largely due to the physical erosion of its habitats and that this erosion may produce suitable habitats for colonization by S. anglica.