bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetics of drought adaptation in Arabidopsis thaliana: I. Pleiotropy contributes to genetic correlations among ecological traits
Authors: Mckay J. K. , Richards J. H. , Mitchell‐Olds T. 
Published: December 2004

AbstractWe examined patterns of genetic variance and covariance in two traits (i) carbon stable isotope ratio δ13C (dehydration avoidance) and (ii) time to flowering (drought escape), both of which are putative adaptations to local water availability. Greenhouse screening of 39 genotypes of Arabidopsis thaliana native to habitats spanning a wide range of climatic conditions, revealed a highly significant positive genetic correlation between δ13C and flowering time. Studies in a range of C3 annuals have also reported large positive correlations, suggesting the presence of a genetically based trade‐off between mechanisms of dehydration avoidance (δ13C) and drought escape (early flowering). We examined the contribution of pleiotropy by using a combination of mutant and near‐isogenic lines to test for positive mutational covariance between δ13C and flowering time. Ecophysiological mutants generally showed variation in δ13C but not flowering time. However, flowering time mutants generally demonstrated pleiotropic effects consistent with natural variation. Mutations that caused later flowering also typically resulted in less negative δ13C and thus probably higher water use efficiency. We found strong evidence for pleiotropy using near‐isogenic lines of FRIGIDA and FLOWERING LOCUS C, cloned loci known to be responsible for natural variation in flowering time. These data suggest the correlated evolution of δ13C and flowering time is explained in part by the fixation of pleiotropic alleles that alter both δ13C and time to flowering.
Statistical phylogeography: methods of evaluating and minimizing inference errors
Authors: Templeton Alan R. 
Published: December 2004

AbstractNested clade phylogeographical analysis (NCPA) has become a common tool in intraspecific phylogeography. To evaluate the validity of its inferences, NCPA was applied to actual data sets with 150 strong a priori expectations, the majority of which had not been analysed previously by NCPA. NCPA did well overall, but it sometimes failed to detect an expected event and less commonly resulted in a false positive. An examination of these errors suggested some alterations in the NCPA inference key, and these modifications reduce the incidence of false positives at the cost of a slight reduction in power. Moreover, NCPA does equally well in inferring events regardless of the presence or absence of other, unrelated events. A reanalysis of some recent computer simulations that are seemingly discordant with these results revealed that NCPA performed appropriately in these simulated samples and was not prone to a high rate of false positives under sampling assumptions that typify real data sets. NCPA makes a posteriori use of an explicit inference key for biological interpretation after statistical hypothesis testing. Alternatives to NCPA that claim that biological inference emerges directly from statistical testing are shown in fact to use an a priori inference key, albeit implicitly. It is argued that the a priori and a posteriori approaches to intraspecific phylogeography are complementary, not contradictory. Finally, cross‐validation using multiple DNA regions is shown to be a powerful method of minimizing inference errors. A likelihood ratio hypothesis testing framework has been developed that allows testing of phylogeographical hypotheses, extends NCPA to testing specific hypotheses not within the formal inference key (such as the out‐of‐Africa replacement hypothesis of recent human evolution) and integrates intra‐ and interspecific phylogeographical inference.
Inbreeding in a natural population of Euodynerus foraminatus (Hymenoptera: Vespidae), a solitary wasp with single‐locus complementary sex determination
Authors: Stahlhut Julie K. , Cowan David P. 
Published: December 2004

AbstractThe solitary wasp Euodynerus foraminatus has single‐locus complementary sex determination (sl‐CSD), which is normally incompatible with inbreeding because it increases the production of sterile or inviable diploid males. Previous field observations of E. foraminatus have suggested that high levels of sibling mating are present in this species. However, conclusions about inbreeding and its genetic consequences could be flawed if based solely upon behavioural observations. Through microsatellite DNA genotyping of 102 E. foraminatus females in southwest Michigan, we estimate that between 55% and 77% of the matings in this population take place between siblings, but the frequency of diploid males is lower than expected. Our data suggest that a mixture of inbreeding and outbreeding persists in E. foraminatus despite the presence of sl‐CSD.
Gene flow in the endophyteNeotyphodiumand implications for coevolution withFestuca arizonica
Authors: Sullivan T. J. , Faeth S. H. 
Published: December 2004

AbstractArizona fescue (Festuca arizonica) often harbours asymptomatic, asexual endophytic fungi from the genusNeotyphodium. In agronomic grasses,Neotyphodiumendophytes are often credited with a wide range of mutualistic benefits to its host many of which are related to fungal production of alkaloids for herbivore deterrence.Neotyphodiumin the native grass Arizona fescue, however, usually produces alkaloids at levels too low to deter herbivores, and in general, does not behave mutualistically. This study uses microsatellite markers to examine rates of gene flow among four Arizona populations ofNeotyphodium. Haplotypic diversity was generally low; only one population contained more than two haplotypes. Haplotypes carrying multiple loci for some or all of the microsatellite loci were also found, indicating a vegetative hybridization event betweenNeotyphodiumand the grass choke pathogen from the genusEpichloë. Gene flow betweenNeotyphodiumpopulations is very low, and likely much lower than the pollen mediated gene flow of its host. These differing rates of gene flow are predicted to create trait mismatching between endophyte and host and may explain the low, or lack of, alkaloid production byNeotyphodiumin Arizona fescue and other native grass species.
‘What's larvae got to do with it?’ Disparate patterns of post‐glacial population structure in two benthic marine gastropods with identical dispersal potential
Authors: Marko P. B. 
Published: December 2004

AbstractIn marine environments, many species have apparently colonized high latitude regions following the last glacial maximum (LGM) yet lack a life‐history stage, such as a free‐living larva, that is clearly capable of long‐distance dispersal. Two hypotheses can explain the modern high latitude distributions of these marine taxa: (1) survival in northern refugia during the LGM or (2) rapid post‐glacial dispersal by nonlarval stages. To distinguish these two scenarios, I characterized the genetic structure of two closely related northeastern Pacific gastropods that lack planktonic larvae but which have distributions extending more than 1000 km north of the southern limit of glaciers at the LGM. Despite having identical larval dispersal potential, these closely related species exhibit fundamentally different patterns of genetic structure. InNucella ostrina, haplotype diversity among northern populations (British Columbia and Alaska) is low, no pattern of isolation by distance exists and a coalescent‐based model of population growth indicates that during the LGM population size was reduced to less than 35% of its current size. In the congeneric and often sympatricN. lamellosa, northern populations harbour a diversity of ancient private haplotypes, significant evidence of isolation by distance exists and regional subdivision was found between northern (Alaska) and southern (southern British Columbia, Washington and Oregon) populations. Estimates of coalescent parameters indicate only a modest reduction in population size during the LGM and that northern and southern populations ofN. lamellosasplit ∼50 Kyr before the LGM. The patterns are consistent with the hypothesis thatN. ostrinarecently reinvaded the northeastern Pacific butN. lamellosasurvived the LGM in a northern refuge. A comparison of similar studies in this region indicates that depleted levels of genetic variation at high latitudes — evidence suggestive of recent colonization from a southern refuge — is more common among intertidal species that live relatively high on the shore, where exposure times to cold stress in air are longer than for species living lower on the shore. These data suggest that for some faunas, ecological differences between taxa may be more important than larval dispersal potential in determining species’ long‐term biogeographical responses to climate change.
Phylogeographical patterns of genetic divergence and speciation in African mole‐rats (Family: Bathyergidae)
Authors: Faulkes C. G. , Verheyen E. , Verheyen W. , Jarvis J. U. M. , Bennett N. C. 
Published: December 2004

AbstractAfrican mole‐rats are subterranean Hystricomorph rodents, distributed widely throughout sub‐Saharan Africa, and displaying a range of social and reproductive strategies from solitary dwelling to the ‘insect‐like’ sociality of the naked mole‐rat, Heterocephalus glaber. Both molecular systematic studies of Rodentia and the fossil record of bathyergids indicate an ancient origin for the family. This study uses an extensive molecular phylogeny and mitochondrial cytochrome b and 12s rRNA molecular clocks to examine in detail the divergence times, and patterns of speciation of the five extant genera in the context of rift valley formation in Africa. Based on a value of 40–48 million years ago (Myr) for the basal divergence of the family (Heterocephalus), we estimate divergence times of 32–40 Myr for Heliophobius, 20–26 Myr for Georychus/Bathyergus and 12–17 Myr for Cryptomys, the most speciose genus. While early divergences may have been independent of rifting, patterns of distribution of later lineages may have been influenced directly by physical barriers imposed by the formation of the Kenya and Western Rift, and indirectly by accompanying climatic and vegetative changes. Rates of chromosomal evolution and speciation appear to vary markedly within the family. In particular, the genus Cryptomys appears to have undergone an extensive radiation and shows the widest geographical distribution. Of the two distinct clades within this genus, one exhibits considerable karyotypic variation while the other does not, despite comparatively high levels of sequence divergence between some taxa. These different patterns of speciation observed both within the family and within the genus Cryptomys may have been a result of environmental changes associated with rifting.
Population genetics of the potentially invasive African fruit fly species,Ceratitis rosaandCeratitis fasciventris(Diptera: Tephritidae)
Authors: Baliraine F. N. , Bonizzoni M. , Guglielmino C. R. , Osir E. O. , Lux S. A. , Mulaa F. J. , Gomulski L. M. , Zheng L. , Quilici S. , Gasperi G. , Malacrida A. R. 
Published: December 2004

AbstractA set of 10 microsatellite markers was used to survey the levels of genetic variability and to analyse the genetic aspects of the population dynamics of two potentially invasive pest fruit fly species,Ceratitis rosaandC. fasciventris,in Africa. The loci were derived from the closely related species,C. capitata. The degree of microsatellite polymorphism inC. rosaandC. fasciventriswas extensive and comparable to that ofC. capitata. InC. rosa, the evolution of microsatellite polymorphism in its distribution area reflects the colonization history of this species. The mainland populations are more polymorphic than the island populations. Low levels of differentiation were found within the Africa mainland area, while greater levels of differentiation affect the islands.Ceratitis fasciventrisis a central–east African species. The microsatellite data over the Uganda/Kenya spatial scale suggest a recent expansion and possibly continuing gene flow within this area. The microsatellite variability data fromC. rosaandC. fasciventris, together with those ofC. capitata, support the hypothesis of an east African origin of theCeratitisspp.
Strong population structure in the marine sponge Crambe crambe (Poecilosclerida) as revealed by microsatellite markers
Authors: Duran S. , Pascual M. , Estoup A. , Turon X. 
Published: December 2004

AbstractDifferent categories of molecular markers have been used so far to study the population structure of sponges. However, these markers often did not have the resolution power to address precisely questions on structuring processes, especially at the intrapopulational level. In this study we show that microsatellites fulfil these expectations, allowing a fine description of population structure at different geographical scales in the marine sponge Crambe crambe. Specimens were collected in 11 locations, representing most of the Atlanto‐Mediterranean range of the species, and were analysed at six loci. As expected for a sessile invertebrate with lecitotrophic larvae, high levels of between‐population structure were found (FST = 0.18) and a significant isolation‐by‐distance pattern was observed. A strong genetic structure was also found within sampled sites (FIS = 0.21) that may be explained by several factors including inbreeding, selfing and the Wahlund effect. In spite of a sampling design planned to avoid the sampling of clones, genotypically identical individuals for the six loci were found in some locations. The significance of these potential clones is discussed and their effect on the observed pattern of population structure assessed. Patterns of allelic distribution within populations suggest the possibility of a recent colonization of the Atlantic range from the Mediterranean Sea.
Comparative analysis of prototype two‐component systems with either bifunctional or monofunctional sensors: differences in molecular structure and physiological function
Authors: Alves Rui , Savageau Michael A. 
Published: December 2004

SummarySignal transduction by a traditional two‐component system involves a sensor protein that recognizes a physiological signal, autophosphorylates and transfers its phosphate, and a response regulator protein that receives the phosphate, alters its affinity toward specific target proteins or DNA sequences and causes change in metabolic activity or gene expression. In some cases the sensor protein, when unphosphorylated, has a positive effect upon the rate of dephosphorylation of the regulator protein (bifunctional sensor), whereas in other cases it has no such effect (monofunctional sensor). In this work we identify structural and functional differences between these two designs. In the first part of the paper we use sequence data for two‐component systems from several organisms and homology modelling techniques to determine structural features for response regulators and for sensors. Our results indicate that each type of reference sensor (bifunctional and monofunctional) has a distinctive structural feature, which we use to make predictions regarding the functionality of other sensors. In the second part of the paper we use mathematical models to analyse and compare the physiological function of systems that differ in the type of sensor and are otherwise equivalent. Our results show that a bifunctional sensor is better than a monofunctional sensor both at amplifying changes in the phosphorylation level of the regulator caused by signals from the sensor and at attenuating changes caused by signals from small phosphodonors. Cross‐talk to or from other two‐component systems is better suppressed if the transmitting sensor is monofunctional, which is the more appropriate design when such cross‐talk represents pathological noise. Cross‐talk to or from other two‐component systems is better amplified if the transmitting sensor is bifunctional, which is the more appropriate design when such cross‐talk represents a physiological signal. These results provide a functional rationale for the selection of each design that is consistent with available experimental evidence for several two‐component systems.
Functional regulation of the Listeria monocytogenes bacteriophage A118 holin by an intragenic inhibitor lacking the first transmembrane domain
Authors: Vukov Nataša , Moll Isabella , Bläsi Udo , Scherer Siegfried , Loessner Martin J. 
Published: December 2004

SummaryWe have dissected the functional properties of the holin encoded by Listeria monocytogenes bacteriophage A118. Native hol118 was cloned into λΔSthf, devoid of the S holin, and tested in an E. coli background. Surprisingly, it caused very late cell lysis, beginning at 80 min after induction. Immunological analyses demonstrated that Hol118 appears in the cytoplasmic membrane shortly after infection. The hol118 gene features a dual start motif similar to λ S. Therefore, different N‐terminally modified Hol118 variants were tested. However, in contrast to λ S, inactivation of AUG‐1 or AUG‐2 showed no significant influence on lysis timing. In addition, Hol118‐mediated lysis could not be triggered by energy poisons, indicating a functional regulation different from that of S. Toeprinting assays on hol118 mRNA revealed an unexpected translational start codon (AUG‐3) at nucleotide position 40. We demonstrated by in vitro and in vivo approaches that the predicted Hol118(83) product is actually produced together with the full‐length polypeptide. However, although the truncated holin lacking its first transmembrane domain appeared in the cytoplasmic membrane, it was shown to be functionally deficient and unable to support λ R‐mediated lysis. In contrast, specific mutations introduced to abolish translation initiation at AUG‐3 drastically accelerated lysis, pointing to an inhibitor function of Hol118(83). This hypothesis was supported by the observation that hol118(83) inhibited holin function when expressed in trans. A deviation from the λ S paradigm is proposed, which represents a new model of holin functional regulation: the intragenic, in frame translated Hol118(83) product, which is devoid of its first transmembrane domain, acts as a functional inhibitor and constitutes a key part of the lysis clock of A118. Presence of the dominant inhibitor function also explains the long latent period of A118, where the onset of lysis takes about 70 min, more than twice the time needed by λ.
Dimerization of the quorum sensing regulator RhlR: development of a method using EGFP fluorescence anisotropy
Authors: Ventre Isabelle , Ledgham Fouzia , Prima Valérie , Lazdunski Andrée , Foglino Maryline , Sturgis James N. 
Published: December 2004

SummaryOf considerable interest in the biology of pathogenic bacteria are the mechanisms of intercellular signalling that can lead to the formation of persistent infections. In this article, we have examined the intracellular behaviour of a Pseudomonas aeruginosa quorum sensing regulator RhlR believed to be important in this process. We have further examined the modulation of this behaviour in response to various auto‐inducers. For these measurements, we have developed an assay based on the fluorescence anisotropy of EGFP fusion proteins that we use to measure protein–protein interactions in vivo. We show that the transcriptional regulator, RhlR, expressed as an EGFP fusion protein in Escherichia coli, forms a homodimer. This homodimer can be dissociated into monomers by the auto‐inducer N‐(3‐oxododecanoyl)‐l‐homoserine lactone (3O‐C12‐HSL) whereas N‐(butanoyl)‐l‐homoserine lactone (C4‐HSL) has little effect. These observations are of particular interest as RhlR modulation of gene expression depends on the presence of C4‐HSL, whereas 3O‐C12‐HSL modulates the expression of genes regulated by LasR. These observations thus provide a framework for understanding the regulatory network that links the various different QS regulators in P. aeruginosa. Furthermore, the technique we have developed should permit the study of numerous protein/protein or protein/nucleic acid interactions in vivo and so shed light on natural protein function.
TupA, the Penicillium marneffei Tup1p homologue, represses both yeast and spore development
Authors: Todd Richard B. , Greenhalgh Jennifer R. , Hynes Michael J. , Andrianopoulos Alex 
Published: December 2004

SummaryFungal pathogenesis is frequently associated with dimorphism – morphological changes between yeast and filamentous forms. Penicillium marneffei, an opportunistic human pathogen, exhibits temperature‐dependent dimorphism, with growth at 25°C as filamentous multinucleate hyphae switching at 37°C to uninucleate yeast cells associated with intracellular pathogenesis. The filamentous hyphae also undergo asexual development generating uninucleate spores, the infectious propagules. Both processes require a switch to coupled nuclear and cell division. Homologous regulators, including Tup1p/GROUCHO‐related WD40 repeat transcription factors, control dimorphism in Candida albicans and asexual development in Aspergillus nidulans. Unlike these fungi, P. marneffei has both developmental programmes allowing examination of common and programme‐specific controls. We show that deletion of tupA, the P. marneffei TUP1 homologue, confers reduced filamentation and inappropriate yeast morphogenesis at 25°C, in stark contrast to constitutive filamentation observed when C. albicans TUP1 is deleted. Deletion of tupA also confers premature brlA‐dependent asexual development, unlike reduced asexual development in the corresponding A. nidulans rcoA deletion mutant. Furthermore, the A. nidulans rcoA deletion mutant is self‐sterile, and we show that tupA from P. marneffei, which lacks an apparent sexual cycle, complements both the asexual and sexual development phenotypes. Therefore, TupA coordinates cell fate by promoting filamentation and repressing both spore and yeast morphogenetic programmes.
Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli
Authors: Bordi Christophe , Théraulaz Laurence , Méjean Vincent , Jourlin‐Castelli Cécile 
Published: December 2004

SummaryThe torCAD operon encoding the TMAO reductase respiratory system is induced in the presence of TMAO by the two‐component regulatory system TorS/TorR. The TorS sensor detects TMAO and transphosphorylates the TorR response regulator via a four‐step phosphorelay. Once phosphorylated, TorR activates expression of the torCAD structural operon. In order to identify new genes regulated by the Tor regulatory system, we performed a genome‐wide transcriptional analysis by using the DNA array technology. We identified seven new transcriptional units whose expression is modulated by the TorS/TorR phosphorelay system. One unit, tnaLAB, is positively regulated whereas the other six, gadA, gadBC, hdeAB, hdeD, yhiE and yhiM, are negatively regulated by this system. Interestingly, the products of some of these units seem to play a role in the survival of E. coli in conditions of extreme pH. The TnaA tryptophanase has been proposed to counteract alkaline stress, whereas the GadA and GadB glutamate decarboxylases and the HdeA and HdeB proteins are involved in the defence against acid stress. Our hypothesis is that the TorS/TorR phosphorelay triggers alkaline‐stress defence to limit alkalinization resulting from the reduction of TMAO in alkaline TMA by the Tor respiratory system. The fact that a ΔtnaLAB mutant showed a dramatic decrease in survival as a result of TMAO respiration is in agreement with such a model. As regulation of these genes by the TorS/TorR system does not depend on pH modification but rather on the presence of TMAO, we propose that E. coli anticipates alkalinization of the medium due to TMA production by base‐resistance gene activation and acid‐resistance gene repression.