bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mucosa‐associated bacteria in ulcerative colitis before and after antibiotic combination therapy
Authors: Nomura T. , Ohkusa T. , Okayasu I. , Yoshida T. , Sakamoto M. , Hayashi H. , Benno Y. , Hirai S. , Hojo M. , Kobayashi O. , Terai T. , Miwa H. , Takei Y. , Ogihara T. , Sato N. 
Published: April 2005

SummaryBackground : We proposed that Fusobacterium varium is one of the causative agents in ulcerative colitis.Aim : To examine the efficacy of antibiotic combination therapy against F. varium and to investigate the mucosa‐associated bacteria before and after the therapy using a new molecular approach.Methods : Twenty patients with ulcerative colitis were randomly assigned into the antibiotic treatment group (amoxicillin, tetracycline and metronidazole for 2 weeks) and no‐antibiotics group. Clinical assessment, colonoscopic and histological evaluations were performed at 0 and 3–5 months after the treatment. DNA from mucosal bacteria was isolated from biopsy specimens. We investigated the mucosa‐associated bacterial components by terminal restriction fragment length polymorphism with the restriction enzyme HhaI and MspI, and quantified the change in the number of bacteria by real‐time polymerase chain reaction. Immunohistochemical detection of F. varium in biopsy specimens was also performed.Results : After the treatment, the clinical assessment, colonoscopic and histological scores improved in the antibiotic group compared with the control group. Three peaks of terminal restriction fragment length polymorphism decreased after treatment only in the antibiotic group. Eubacterium rectale, Dorea formicigenerans, Clostridium clostridioforme and F. varium were included in these peaks. Based on the real‐time polymerase chain reaction study, only F. varium was significantly reduced after treatment. In the immunostaining, post‐treatment scores in treatment group were significantly lower than that in control group.Conclusions : Antibiotics combination therapy was effective for ulcerative colitis. The number of mucosa‐associated F. varium significantly decreased after the treatment.
A multilocus population genetic survey of the greater sage‐grouse across their range
Authors: OYLER‐MCCANCE S. J. , TAYLOR S. E. , QUINN T. W. 
Published: April 2005

AbstractThe distribution and abundance of the greater sage‐grouse (Centrocercus urophasianus) have declined dramatically, and as a result the species has become the focus of conservation efforts. We conducted a range‐wide genetic survey of the species which included 46 populations and over 1000 individuals using both mitochondrial sequence data and data from seven nuclear microsatellites. Nested clade andstructureanalyses revealed that, in general, the greater sage‐grouse populations follow an isolation‐by‐distance model of restricted gene flow. This suggests that movements of the greater sage‐grouse are typically among neighbouring populations and not across the species, range. This may have important implications if management is considering translocations as they should involve neighbouring rather than distant populations to preserve any effects of local adaptation. We identified two populations in Washington with low levels of genetic variation that reflect severe habitat loss and dramatic population decline. Managers of these populations may consider augmentation from geographically close populations. One population (Lyon/Mono) on the southwestern edge of the species’ range appears to have been isolated from all other greater sage‐grouse populations. This population is sufficiently genetically distinct that it warrants protection and management as a separate unit. The genetic data presented here, in conjunction with large‐scale demographic and habitat data, will provide an integrated approach to conservation efforts for the greater sage‐grouse.
Genetic continuity of brood‐parasitic indigobird species
Authors: SEFC KRISTINA M. , PAYNE ROBERT B. , SORENSON MICHAEL D. 
Published: April 2005

AbstractSpeciation in brood‐parasitic indigobirds (genus Vidua) is a consequence of behavioural imprinting in both males and females. Mimicry of host song by males and host fidelity in female egg laying result in reproductive isolation of indigobirds associated with a given host species. Colonization of new hosts and subsequent speciation require that females occasionally lay eggs in the nests of novel hosts but the same behaviour may lead to hybridization when females parasitize hosts already associated with other indigobird species. Thus, retained ancestral polymorphism and ongoing hybridization are two alternative explanations for the limited genetic differentiation among indigobird species. We tested for genetic continuity of indigobird species using mitochondrial sequences and nuclear microsatellite data. Within West Africa and southern Africa, allopatric populations of the same species are generally more similar to each other than to sympatric populations of different species. Likewise, a larger proportion of genetic variation is explained by differences between species than by differences between locations in alternative hierarchical amovas, suggesting that the rate of hybridization is not high enough to homogenize sympatric populations of different species or prevent genetic differentiation between species. Broad sharing of genetic polymorphisms among species, however, suggests that some indigobird species trace to multiple host colonization events in space and time, each contributing to the formation of a single interbreeding population bound together by songs acquired from the host species.
Northwestern song sparrow populations show genetic effects of sequential colonization
Authors: PRUETT CHRISTIN L. , WINKER KEVIN 
Published: April 2005

AbstractTwo genetic consequences are often considered evidence of a founder effect: substantial loss in genetic diversity and rapid divergence between source and founder populations. Single‐step founder events have been studied for these effects, but with mixed results, causing continued controversy over the role of founder events in divergence. Experiments of serial bottlenecks have shown losses of diversity, increased divergence, and rapid behavioural changes possibly leading to reproductive isolation between source and final populations. The few studies conducted on natural, sequentially founded systems show some evidence of these effects. We examined a natural vertebrate system of sequential colonization among northwestern song sparrows (Melospiza melodia). This system has an effectively linear distribution, it was probably colonized within the last 10 000 years, there are morphological and behavioural differences among populations, and the westernmost populations occur in atypical habitats for the species. Eight microsatellite loci from eight populations in Alaska and British Columbia (n = 205) showed stepwise loss of genetic diversity, genetic evidence for strong population bottlenecks, and increased population divergence. The endpoint population on Attu Island has extremely low diversity (HE = 0.18). Our study shows that sequential bottlenecks or founder events can have powerful genetic effects in reducing diversity, possibly leading to rapid evolutionary divergence.
Transposable element polymorphism of Wolbachia in the mosquito Culex pipiens: evidence of genetic diversity, superinfection and recombination
Authors: DURON OLIVIER , LAGNEL JACQUES , RAYMOND MICHEL , BOURTZIS KOSTAS , FORT PHILIPPE , WEILL MYLÈNE 
Published: April 2005

Abstract Wolbachia is a group of maternally inherited endosymbiotic bacteria that infect and induce cytoplasmic incompatibility (CI) in a wide range of arthropods. In contrast to other species, the mosquito Culex pipiens displays an extremely high number of CI types suggesting differential infection by multiple Wolbachia strains. Attempts so far failed to detect Wolbachia polymorphism that might explain this high level of CI diversity found in C. pipiens populations. Here, we establish that Wolbachia infection is near to or at fixation in worldwide populations of the C. pipiens complex. Wolbachia polymorphism was addressed by sequence analysis of the Tr1 gene, a unique transposable element of the IS5 family, which allowed the identification of five C. pipiens Wolbachia strains, differing either by nucleotide substitution, presence or absence pattern, or insertion site. Sequence analysis also showed that recombination, transposition and superinfection occurred at very low frequencies. Analysis of the geographical distributions of each Wolbachia strain among C. pipiens populations indicated a strong worldwide differentiation independent from mosquito subspecies type, except in the UK. The availability of this polymorphic marker now opens the way to investigate evolution of Wolbachia populations and CI dynamics, in particular in regions where multiple crossing types coexist among C. pipiens populations.
Similar mating and sperm displacement patterns in two highly divergent D. simulans populations from Africa and Europe
Authors: SCHLÖTTERER CHRISTIAN , REISS MARTINA , SCHNEIDER ANGELIKA , IMHOF MARIANNE 
Published: April 2005

AbstractThe frequency of remating in Drosophila melanogaster is affected by both genetic and ecological factors. We studied the remating behaviour in one European (Italy) and one African (Uganda) Drosophila simulans population using six highly polymorphic microsatellite markers. Despite that the populations were genetically distinct (FST = 0.18) and originated from very dissimilar ecological settings with different population densities, we inferred a very similar mating pattern. The remating parameter α was similar in both populations (ā = 1.3–1.4). No more than two distinct paternal genotypes per family were detected in each population.
Geographic variation of multiple paternity in the American lobster, Homarus americanus
Authors: GOSSELIN THIERRY , SAINTE‐MARIE BERNARD , BERNATCHEZ LOUIS 
Published: April 2005

AbstractWe studied the frequency of multiple paternity for American lobster (Homarus americanus) at three Canadian sites differing in exploitation rate and mean adult size. The probability of detecting multiple paternity using four microsatellite loci and 100 eggs per female was in excess of 99% under various scenarios of paternal contribution. Overall, 13% of the 108 examined females carried a clutch sired by two or three males. Multiple paternity was observed at the two most exploited sites (11% at Magdalen Islands and 28% at Grand Manan Island), whereas single paternity only was observed at the least exploited site (Anticosti Island). Within populations females with a clutch sired by more than one male tended to be smaller than females with a clutch sired by a single male. Based on these and other findings, we postulate a link between female promiscuity and sperm limitation in the American lobster.
Postglacial expansion of the southern red‐backed vole (Clethrionomys gapperi) in North America
Authors: RUNCK AMY M. , COOK JOSEPH A. 
Published: April 2005

AbstractDynamic climatic oscillations of the Pleistocene dramatically changed the distributions of high latitude species. Molecular investigations of a variety of organisms show that processes of postglacial colonization of boreal regions were more complex than initially thought. Phylogeographical and coalescent analyses were conducted on partial sequences of the cytochrome b gene (600 bp) from 64 individuals of Clethrionomys gapperi from North Carolina, Pennsylvania, Minnesota, Idaho, Washington, British Columbia, Northwest Territories, and Alaska to test hypotheses relating to Pleistocene refugia and postglacial colonization routes. Three divergent clades (east, west, central) were identified with highest net divergence (dA = 5.2%) between the eastern and western clades. Populations from the recently deglaciated higher latitudes of Canada and Alaska are closely related to lower latitude populations of the central clade (dA = 1.2%) suggesting recent expansion from this midwestern region. No representatives from the east or west clade were found at latitudes higher than 50°N, indicating that postglacial colonization occurred through a midcontinental route. The high latitude population from the Northwest Territories exhibited demographic patterns and genetic diversity consistent with a stable noncolonizing population. This population is found near the Mackenzie range, where the two continental ice sheets were believed to have coalesced. Molecular variation observed in this population may be the result of leading edge population diversifying in the continental corridor or may reflect the signal of a high latitude refugial population.
Spatial structure of genetic variation and primary succession in the pioneer tree species Antirhea borbonica on La Réunion
Authors: LITRICO I. , RONFORT J. , VERLAQUE R. , THOMPSON J. D. 
Published: April 2005

AbstractIn habitats where colonization and extinction are recurrent, the distribution of gene frequencies among patches of suitable habitat may reflect the age structure of different populations. In this study, we quantify population genetic structure for a pioneer tree species, Antirhea borbonica, in a chrono‐sequence of primary succession on the lava flows of the Piton de La Fournaise volcano (La Réunion). Using microsatellite loci and amplified fragment length polymorphism (AFLP) markers, we quantified genetic variation within and among populations for early‐ and late‐succession populations in a landscape where extinction and recolonization are recurrent (the ‘Grand Brûlé’) and for late‐succession populations in a more stable landscape. This study produced three main results. First, we detected no evidence that founder events increase genetic differentiation among colonizing populations; FST values among early‐ and among late‐succession populations were similar. Second, we found no evidence for isolation by distance; genetic distance was not correlated with spatial distance within and among populations. Third, FIS values are consistently high in all populations, despite the fact that A. borbonica populations are functionally close to dioecy and thus expected to have an outcrossing mating system. Multiple colonization events from different sources may limit differentiation among young populations and spatial isolation may enhance differentiation among late‐succession populations. Ecological processes acting during colonization may create the conditions for spatial aggregation within pioneer populations, and thus contribute to the high FIS values.
On the origins of extreme mycorrhizal specificity in the Monotropoideae (Ericaceae): performance trade‐offs during seed germination and seedling development
Authors: BIDARTONDO M. I. , BRUNS T. D. 
Published: April 2005

AbstractFungal‐induced seed germination is a phenomenon characteristic of mycorrhizal plants that produce dust‐like seeds with only minimal nutritional reserves. In such systems, fungi trigger germination and/or subsidize development. We studied mycorrhizal germination in relation to mycorrhizal specificity in the Monotropoideae, a lineage of dust‐seeded nonphotosynthetic plants that are dependent upon ectomycorrhizal fungi of forest trees. A total of 1695 seed packets, each containing two to five compartments with seeds from different sources, were buried for up to 2 years near known ectomycorrhizal fungi in six different native forest locations. Upon harvest, seedlings were analysed by cultivation‐independent molecular methods to identify their mycorrhizal fungi. We report that (i) germination is only induced by the same fungus that associates with mature plants or by closely related congeners; (ii) seedlings associated with the latter fungi develop less than those associated with maternal fungal species in most settings; and (iii) exceptions to this pattern occur in allopatric settings, where novel plant–fungal associations can result in the greatest seedling development. We interpret these results as evidence of performance trade‐offs between breadth of host range and rate of development. We propose that in conjunction with host‐derived germination cues, performace trade‐offs can explain the extreme mycorrhizal specificity observed at maturity. The allopatric exceptions support the idea that performance trade‐offs may be based on a coevolutionary arms race and that host range can be broadened most readily when naïve fungal hosts are encountered in novel settings.
Genetic analysis of the breeding system of an invasive subterranean termite, Reticulitermes santonensis, in urban and natural habitats
Authors: DRONNET STÉPHANIE , CHAPUISAT MICHEL , VARGO EDWARD L. ,   CAROLINE LOHOU, BAGNÈRES ANNE‐GENEVIÈVE 
Published: April 2005

Abstract Reticulitermes santonensis is a subterranean termite that invades urban areas in France and elsewhere where it causes damage to human‐built structures. We investigated the breeding system, colony and population genetic structure, and mode of dispersal of two French populations of R. santonensis. Termite workers were sampled from 43 and 31 collection points, respectively, from a natural population in west–central France (in and around the island of Oléron) and an urban population (Paris). Ten to 20 workers per collection point were genotyped at nine variable microsatellite loci to determine colony identity and to infer colony breeding structure. There was a total of 26 colonies, some of which were spatially expansive, extending up to 320 linear metres. Altogether, the analysis of genotype distribution, F‐statistics and relatedness coefficients suggested that all colonies were extended families headed by numerous neotenics (nonwinged precocious reproductives) probably descended from pairs of primary (winged) reproductives. Isolation by distance among collection points within two large colonies from both populations suggested spatially separated reproductive centres with restricted movement of workers and neotenics. There was a moderate level of genetic differentiation (FST = 0.10) between the Oléron and Paris populations, and the number of alleles was significantly higher in Oléron than in Paris, as expected if the Paris population went through bottlenecks when it was introduced from western France. We hypothesize that the diverse and flexible breeding systems found in subterranean termites pre‐adapt them to invade new or marginal habitats. Considering that R. santonensis may be an introduced population of the North American species R. flavipes, a breeding system consisting primarily of extended family colonies containing many neotenic reproductives may facilitate human‐mediated spread and establishment of R. santonensis in urban areas with harsh climates.
Allopatric origins of sympatric brook charr populations: colonization history and admixture
Authors: FRASER D. J. , BERNATCHEZ L. 
Published: April 2005

AbstractNatural selection is presumed to be the driving force behind the occurrence of phenotypically and genetically divergent populations in sympatry within many north temperate freshwater fishes. If, however, these populations have different ancestral origins, history could also contribute to their divergence. We previously found evidence for the role of selection in the evolution of divergent outflow and inflow breeding populations of migratory brook charr (Salvelinus fontinalis) inhabiting postglacial Mistassini Lake (Québec, Canada). Here, we show that these populations do not have a common origin, through the use of admixture and spatial analyses with seven microsatellite loci. Divergent populations clustered into two different population groups when compared to samples from surrounding drainages, although inflow populations appeared to be more admixed between the two population groups than the outflow population. These results are noteworthy since outflow and inflow populations were monomorphic at mitochondrial DNA (338‐bp sequence of the control region) and are only moderately differentiated (meanFST = 0.10). Colonization by two ancestral populations was also consistent with known outflow direction changes throughout lake formation. In addition to providing insight into how phenotypic divergence in sympatry may have been affected by the nature (i.e. timing and direction) of colonization of ancestral populations, our results also suggest that ancestral populations may have differed in their ability to colonize certain lake habitats.
Phylogeographic analysis of mitochondrial gene flow and introgression in the salamander,Plethodon shermani
Authors: WEISROCK D. W. , KOZAK K. H. , LARSON A. 
Published: April 2005

AbstractPlethodon shermanicomprises a series of geographically disjunct populations occupying high‐elevation mountain isolates. These populations hybridize at their borders with salamanders of thePlethodon glutinosusspecies complex, and past range expansions inferred from Pleistocene climatic cycles may have increased the possible genetic interactions betweenP. shermaniand species of theP. glutinosuscomplex. Because mitochondrial DNA haplotypes often show introgression across species borders, we survey mtDNA variation for evidence of past and ongoing genetic interactions betweenP. shermani,its close relativePlethodon cheoah,and species of theP. glutinosuscomplex. Ongoing hybridization with theP. glutinosus‐complex speciesPlethodon teyahaleeis accompanied by extensive mitochondrial introgression in some Unicoi populations ofP. shermani,but it has little genetic impact onP. shermanipopulations outside hybrid zones at three other isolates (Tusquitee, Wayah Bald, Standing Indian). Some Unicoi populations ofP. shermaniexhibit mtDNA evidence of past hybridization with diverse lineages fromP. aureolusandP. glutinosus. The Tusquitee isolate ofP. shermaniis also characterized by mtDNA haplotypes most closely related toPlethodon aureolusandP. glutinosus, presumably introduced by past genetic contact with these species or with introgressed populations of UnicoiP. shermani. The mtDNA variation in sampled populations of the Wayah Bald and Standing Indian isolates ofP. shermaniappears largely unaffected by ongoing hybridization. Principal components analyses of allozymic data indicate thatP. shermaniisolates collectively form a genetically homogeneous unit clearly demarcated from species with which they have had current or past genetic interactions. Rapid mtDNA introgression associated with transient contacts betweenP. shermaniand other species permits a fine‐level resolution of evolutionary lineages not evident from allozymic data.
Monitoring coyote population dynamics by genotyping faeces
Authors: PRUGH L. R. , RITLAND C. E. , ARTHUR S. M. , KREBS C. J. 
Published: April 2005

AbstractReliable population estimates are necessary for effective conservation and management, and faecal genotyping has been used successfully to estimate the population size of several elusive mammalian species. Information such as changes in population size over time and survival rates, however, are often more useful for conservation biology than single population estimates. We evaluated the use of faecal genotyping as a tool for monitoring long‐term population dynamics, using coyotes (Canis latrans) in the Alaska Range as a case study. We obtained 544 genotypes from 56 coyotes over 3 years (2000–2002). Tissue samples from all 15 radio‐collared coyotes in our study area had ≥ 1 matching faecal genotypes. We used flexible maximum‐likelihood models to study coyote population dynamics, and we tested model performance against radio telemetry data. The staple prey of coyotes, snowshoe hares (Lepus americanus), dramatically declined during this study, and the coyote population declined nearly two‐fold with a 11/2‐year time lag. Survival rates declined the year after hares crashed but recovered the following year. We conclude that long‐term monitoring of elusive species using faecal genotyping is feasible and can provide data that are useful for wildlife conservation and management. We highlight some drawbacks of standard open‐population models, such as low precision and the requirement of discrete sampling intervals, and we suggest that the development of open models designed for continuously collected data would enhance the utility of faecal genotyping as a monitoring tool.