A note on the structure of system state spaces and its implications on the existence of non-repeatable experiments

The implication of state space structure on the existence of a repeatable experimentE designed to determine if a states∈L has propertyP or notP is investigated. It is shown that if a state spaceL is connected, then no experimentE is repeatable. This formalism is used to demonstrate that if a propertyP has an associated set of points inL which is dense with dense complement inL, then there exists no repeatable experimentE which can be used to test whethers has propertyP or notP. Other consequences of this formalization are discussed.     

The phylogenetic position of the bumble bee inquiline Bombus inexspectatus and implications for the evolution of social parasitism

The high alpine European bumble bee Bombus (Thoracobombus) inexspectatus is one of three taxa in which obligate social parasitism has evolved in bumble bees. Until now, the phylogenetic placement of this species has not been analyzed quantitatively because it is rare in nature. Here a specimen of B. inexspectatus is sequenced for five genes to assess its phylogenetic position relative to other bumble bee species. Phylogenetic estimation of B. inexspectatus places this species within the subgenus Thoracobombus, as expected based on morphology. This provides strong support for the acquisition of social parasitism in B. inexspectatus separate from that found in the bumble bees of the subgenus Psithyrus and B. (Alpinobombus) hyperboreus. Furthermore, B. inexspectatus is not the sister taxon of its host but is a near relative, suggesting a loose but not strict adherence to Emery’s rule. B. inexspectatus is a sister taxon to a clade including B. veteranus, a frequent nest usurper that has been suggested to be a facultative social parasite. The phylogenetic placement of all bumble bee social parasites relative to their hosts is discussed.     

Tests of Independence and Zero Correlations Among P Random Variables

Suppose it is desired to determine whether there is an association between any pair of p random variables. A common approach is to test H₀ : R = I, where R is the usual population correlation matrix. A closely related approach is to test H₀ : R_pb = I, where R_pb is the matrix of percentage bend correlations. In so far as type I errors are a concern, at a minimum any test of H₀ should have a type I error probability close to the nominal level when all pairs of random variables are independent. Currently, the Gupta-Rathie method is relatively successful at controlling the probability of a type I error when testing H₀: R = I, but as illustrated in this paper, it can fail when sampling from nonnormal distributions. The main goal in this paper is to describe a new test of H₀: R_pb = I that continues to give reasonable control over the probability of a type I error in the situations where the Gupta-Rathie method fails. Even under normality, the new method has advantages when the sample size is small relative to p. Moreover, when there is dependence, but all correlations are equal to zero, the new method continues to give good control over the probability of a type I error while the Gupta-Rathie method does not. The paper also reports simulation results on a bootstrap confidence interval for the percentage bend correlation.     

Genetic polymorphism for cyanogenesis and linkage at the linamarase locus in Trifolium nigrescens Viv. subsp. nigrescens

Polymorphisms at two genetic loci conditioning the cyanogenic glucoside linamarin (Ac) and the glucosidase linamarase (Li) are reported for the first time in Trifolium nigrescens Viv. subspecies nigrescens (2n=2x=16). T. nigrescens is one of several possible ancestral species that may have donated a genome to the allotetraploid species white clover (T. repens L., 2n=4x=32). T. nigrescens is a strong candidate because it is the only very close relative that, like white clover, is cyanogenic. Genetic analysis showed that in T. nigrescens, cyanogenesis was inherited as a two-locus genetic system in a similar way to that in white clover. Furthermore, Li, which is linked to the locus Sdh (shikimate dehydrogenase, SDH) at a distance of 6 cM in one genome of white clover, also showed linkage (12 cM) in T. nigrescens. It is concluded that one of the subspecies of T. nigrescens is a likely donor of a genome to white clover. Received: 27 December 2000 / Accepted: 12 April 2001     

The regulation of urease activity in Aspergillus nidulans

Aspergillus nidulans can utilize urea as a sole source of nitrogen but not as a carbon source. Urea is degraded by a urease. Mutation at any one of three genes, ureB, ureC, and ureD, may result in deficient urease activity. The ureB gene is closely linked to ureA, the structural gene for the urea transport protein. The heat lability of a ureB ^– revertant strain, intragenic complementation tests, and the linkage of ureB to ureA suggest that ureB is the urease structural gene. The ureD gene is probably involved in the synthesis or incorporation of a nickel cofactor essential for urease activity. The function of the ureC gene is not known. Urease is not induced but is subject to nitrogen regulation. The urease activities of ammonium-derepressed mutants show that the effector of nitrogen regulation is more likely to be glutamine than ammonium. When glutamine is present in the medium, urease appears to be inactivated by some means which does not involve a newly synthesized protease or a direct interaction between glutamine and urease.     

Extinction times and phase transitions for spatially structured closed epidemics

This paper considers the time to extinction for a stochastic epidemic model of SEIR form without replacement of susceptibles. It first shows how previous rigorous results can be heuristically explained in terms of the more transparent dynamics of an approximating deterministic system. The model is then extended to include a host population structured into patches, with weak nearest-neighbour mixing of infection. It is shown, by considering the approximating deterministic system, that the expected time to extinction in a population of n + 1 patches each of size N is of the form a log N + bn, provided that N > N _c where N _c is a critical patch size below which transits are unlikely to occur. This corresponds to the simple decomposition of the time of an epidemic into the time it takes to spread through one patch plus the time it takes to transit to each of n successive patches. Expressions for this threshold and the coefficients of the time to extinction are given in terms of the transmission parameters of infection and the coupling strength between patches. These expressions are compared with numerical results using parameters relevant to a study of phocine distemper virus in North Sea seals, and the agreement is found to be good for large and small N. In the region when N ≈ N _c , where transits may or may not occur, interesting transitional behaviour is seen, leading to a non-monotonicity of the extinction time as a function of N.     

A cladistic analysis of Erythracarinae (Acarina: Prostigmata: Anystidae), with the description of a new genus

A cladistic analysis of sixty erythracarine species is presented and used to justify recent nomenclatorial changes to the classification of erythracarine genera. Erythracarinae is redescribed, and a new diagnosis for the subfamily and a key to the included genera are presented. Neotarsolarcus is recognized as a junior synonym of Tarsolarkus, which is recorded for the first time from North America. A new genus, Pedidromus, with six new species (P. agitatus sp.n. P. curiosus sp.n., P. durongensis sp.n., P. peliculus sp.n., P. pilotrix sp.n., P. velox sp.n.) is described.     

Notes on some rare Dicranaceae

Abstract

Dicranella riparia is shown to be more appropriately treated as Kiaeria riparia comb. nov.; Kiaeria glacialis is shown to be a misfit in Dicranum; Oncophorus sardous is placed in synonymy of O. wahlenbergii; Arctoa anderssonii is shown to be a distinct species.     

Model of a hypothetical protohominid dentition and its implications for hominid phylogeny

The complete dentition of the common ancestor ofAustralopithecus andHomo, intermediate between that of a pongid and a hominid, is virtually unknown. The maxillary dentition (P3-M2) ofRamapithecus brevirostris Lewis, 1934, a pongid from the Early Pliocene, and that of hominids from the Late Pliocene and Plio/Pleistocene is known. SinceR. brevirostris is probably ancestral to the hominids, a model of intermediate maxillary dentition (P3-M2) is extrapolated and described. The model represents a hypothetical protohominid dentition. It does not conform with the teeth ofAustralopithecus, but shows greater morphological affinity to hominine dentition and to 5 myo hominids. TheHomo lineage, therefore, may go back to the Middle Pliocene. According to the normal sequence of evolution, it is most unlikely thatAustralopithecus gave rise toHomo, but much more probable that a very early, generalizedHomo evolved into an advanced, specializedAustralopithecus.     

Control regions within the argECBH gene cluster of Escherichia coli K12

Summary In Escherichia coli K12, four of the nine structural genes involved in the biosynthesis of arginine (argE, C, B and H) form a tight cluster within which a clockwise-polarized unit of expression (argCBH) had previously been identified. From a mutant carrying an argCB deletion that greatly lowers the rate of expression of argE but falls short of known argE markers, we have isolated several derivatives in which the expression of argE is partly restored. In about a third of these strains repression of both E and H enzymes by arginine is almost abolished. The mutations responsible appear to be cis-dominant and to map to the right of argE, probably between argE and C. One mutant in which control of argE alone is affected has also been found; it is shown to carry a duplication of argE in addition to the argCB deletion of the parental strain. We discuss the hypothesis that argE and argCBH form two operons transcribed in opposite directions from an internal promoter-operator complex.It is also suggested that a secondary promoter exists at or near the argB-H boundary.     

Systematic relationships within the Vibrionaceae (Bacteria: Gammaproteobacteria): steps toward a phylogenetic taxonomy

A phylogenetic hypothesis is presented for all 95 species of the family Vibrionaceae (Bacteria: Gammaproteobacteria) based on a combined analysis of eight molecular loci (16S rRNA, gyrB, recA, rpoA, gapA, mreB, topA, atpA) for up to 9337 nucleotide characters. Members of this taxon exhibit diverse life histories, including bioluminescence, pathogenicity to human and marine organisms, symbiosis, quorum sensing and extremophilic environment living, making a hypothesis of phylogenetic history important to studies addressing these traits from an evolutionary perspective. It is proposed that this phylogenetic set of relationships replaces previous phenetic hypotheses and be used to construct a phylogenetic taxonomy. Recent taxonomic proposals, including the validity of four, instead of one, families representing the 95 species and historical notions of genera within the group are compared with the presented phylogenetic hypothesis. Character support is traced through the tree and is used to address these taxonomic proposals. Photobacterium is not a monophyletic group as it is currently delimited. Aliivibrio is found within Photobacterium, suggesting a new definition for Photobacterium that includes all species of Aliivibrio. Enterovibrio, Salinivibrio and Grimontia, previously thought to be distinct from and basal to Photobacterium and Vibrio, are found nested deeply within a large Vibrio clade. © The Willi Hennig Society 2010.     

Molecular phylogeny of Macrolycus (Coleoptera: Lycidae) with description of new species from China

Macrolycus is a genus of net‐winged beetles with 69 species distributed in the eastern Palearctic and northernmost part of the Oriental region. The first molecular phylogeny of Macrolycus was produced using an rrnL + tRNA‐Leu + nad1 mtDNA fragment. The major lineages and species limits were identified with morphology and molecular data. We propose that Cerceros is a subgenus of Macrolycus to enable identification of all adult specimens in the genus without DNA sequencing. Two species groups are proposed in Macrolycus s. str. and six in Cerceros. Additionally, twelve Macrolycus species are newly described from China: M. aquilinus, M. baihualingensis, M. bicolor, M. guangxiensis, M. jianfenglingensis, M. kuatunensis, M. lizipingensis, M. parvus, M. phoeniceus, M. rhodoneurus, M. rosaceus and M. sichuanensis. Macrolycus holzschuhi is proposed to be a junior subjective synonym of M. jeanvoinei. The highest diversity of Macrolycus is found in southern China. The species from the main islands of Japan are placed in two species groups: M. excellens is a sister to remaining species of the M. murzini group and the M. flabellatus group is a monophylum of closely related species in a sister position to the M. bicolor group.     

On the maximal cliques in c-max-tolerance graphs and their application in clustering molecular sequences

Given a set S of n locally aligned sequences, it is a needed prerequisite to partition it into groups of very similar sequences to facilitate subsequent computations, such as the generation of a phylogenetic tree. This article introduces a new method of clustering which partitions S into subsets such that the overlap of each pair of sequences within a subset is at least a given percentage c of the lengths of the two sequences. We show that this problem can be reduced to finding all maximal cliques in a special kind of max-tolerance graph which we call a c-max-tolerance graph. Previously we have shown that finding all maximal cliques in general max-tolerance graphs can be done efficiently in O(n ³ + out). Here, using a new kind of sweep-line algorithm, we show that the restriction to c-max-tolerance graphs yields a better runtime of O(n ² log n + out). Furthermore, we present another algorithm which is much easier to implement, and though theoretically slower than the first one, is still running in polynomial time. We then experimentally analyze the number and structure of all maximal cliques in a c-max-tolerance graph, depending on the chosen c-value. We apply our simple algorithm to artificial and biological data and we show that this implementation is much faster than the well-known application Cliquer. By introducing a new heuristic that uses the set of all maximal cliques to partition S, we finally show that the computed partition gives a reasonable clustering for biological data sets.     

Monophyly and phylogenetic relationships of Minthostachys (Labiatae, Nepetoideae) examined using morphological and nrITS data

Minthostachys (Benth.) Spach (Labiatae) from Andean South America was long held to be closely related to Macaronesian Bystropogon L’Hér. or to North American Pycnanthemum Michx. The possibility of a close relationship to elements of South American Satureja/Clinopodium s.l. is here proposed for the first time, and a phylogenetic analysis of nrITS data is employed to test the competing hypotheses. For Minthostachys and its putative closest relatives, the possible evolution of morphological characters is investigated with a cladistic analysis. The results suggest that Minthostachys is nested in a clade of South American Mentheae, and probably in the former genus Xenopoma Willd., a group of small-flowered, bee-pollinated species currently included in Clinopodium L.. Minthostachys is considered monophyletic based on nrITS data and its scandent habit.     

Taxonomic studies in Chiloscyphus Corda (Jungermanniales: Lophocoleaceae) based on nrITS sequences and morphology

Maximum parsimony and likelihood analyses of 40 Lophocoleaceae nrITS sequences and 6 Plagiochilaceae sequences (outgroup) lead to a robust phylogeny of Chiloscyphus. Four main lineages are assigned to as Chiloscyphus subgenera Chiloscyphus, Lophocolea, Connati and Notholophocolea. Chiloscyphus subgen. Connati is resolved sister to the remainder of this genus. Chiloscyphus subgenus Lophocolea is subdivided into sections Heterophylli (incl. sect. Semiteretes, syn. nov.), Lophocolea, Microlophocolea, and Novae-Zeelandiae. Five accessions of Chiloscyphus pallescens with a chromosome number of n = 18 form a robust monophyletic lineage that is placed sister to a well supported clade with 4 accessions of C. polyanthos [n = 9]. Chiloscyphus mandonii is placed in the synonymy of C. latifolius.     

Lophodermium pini-mugonis sp. nov. on needles of Pinus mugo from the Alps based on morphological and molecular data

Lophodermium pini-mugonis, collected on needles of Pinus mugo from German Alps, is described as a species new to science. It is characterized by subcuticular ascomata with a wrinkled surface and a somewhat untidy outline, a complex structure of lip cells, and ellipsoidal conidia. An analysis of the internal transcribed spaces of rDNA showed that Lophodermium pini-mugonis is, sister to Lophodermium autumnale and distantly related to other Lophodermium species on pines. The hypothesis of cospeciation of Lophodermium species with members of the Pinaceae is discussed.     

Evolution of Phage-Type RNA Polymerases in Higher Plants: Characterization of the Single Phage-Type RNA Polymerase Gene from <Emphasis Type="Italic">Selaginella moellendorffii</Emphasis>

Selaginella moellendorfii (spikemoss) sequence trace data encoding a polypeptide highly similar to angiosperm and moss phage-type organelle RNA polymerases (RpoTs) were used to isolate a BAC clone containing the full-length gene SmRpoT as well as the corresponding cDNA. The SmRpoT mRNA comprises 3452 nt with an open reading frame of 3006 nt, encoding a putative protein of 1002 amino acids with a molecular mass of 113 kDa. The SmRpoT gene comprises 19 exons and 18 introns, conserved in their position with those of the angiosperm and Physcomitrella RpoT genes. In phylogenetic analyses, the Selaginella RpoT polymerase is in a sister position to all other phage-type polymerases of angiosperms. However, according to its conserved exon–intron structure, the Selaginella RpoT gene is representative of the molecular evolutionary lineage giving rise to the RpoT gene family of flowering plants. The N-terminal transit peptide of SmRpoT is shown to confer targeting of green fluorescent protein exclusively to mitochondria after transient expression in Arabidopsis and Selaginella protoplasts. Angiosperms and the moss P. patens possess small gene families encoding RpoTs, which include mitochondrial- and chloroplast-targeted RNA polymerases. In striking contrast, the Selaginella RpoT gene is shown to be single-copy, although Selaginella, as a lycophyte, has a phylogenetic position between Physcomitrella and angiosperms. Thus, there is no evidence that Selaginella may contain a nuclear-encoded phage-type chloroplast RNA polymerase.