bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates
Authors: FAUBET PIERRE , WAPLES ROBIN S. , GAGGIOTTI OSCAR E. 
Published: February 2007

AbstractBayesian methods have become extremely popular in molecular ecology studies because they allow us to estimate demographic parameters of complex demographic scenarios using genetic data. Articles presenting new methods generally include sensitivity studies that evaluate their performance, but they tend to be limited and need to be followed by a more thorough evaluation. Here we evaluate the performance of a recent method, bayesass, which allows the estimation of recent migration rates among populations, as well as the inbreeding coefficient of each local population. We expand the simulation study of the original publication by considering multi‐allelic markers and scenarios with varying number of populations. We also investigate the effect of varying migration rates and FST more thoroughly in order to identify the region of parameter space where the method is and is not able to provide accurate estimates of migration rate. Results indicate that if the demographic history of the species being studied fits the assumptions of the inference model, and if genetic differentiation is not too low (FST ≥ 0.05), then the method can give fairly accurate estimates of migration rates even when they are fairly high (about 0.1). However, when the assumptions of the inference model are violated, accurate estimates are obtained only if migration rates are very low (m = 0.01) and genetic differentiation is high (FST ≥ 0.10). Our results also show that using posterior assignment probabilities as an indication of how much confidence we can place on the assignments is problematical since the posterior probability of assignment can be very high even when the individual assignments are very inaccurate.
Asexual and sexual hybrids betweenFundulus diaphanusandF. heteroclitusin the Canadian Atlantic region
Authors: HERNÁNDEZ CHÁVEZ CECILIA , TURGEON JULIE 
Published: February 2007

AbstractLevels and origins of clonal diversity in asexual hybrid animals are critical to understanding how they can coexist with their sexual progenitor species. In this study, asexual gynogenetic hybrids betweenFundulus diaphanusandFundulus heteroclitusknown from two sites in Nova Scotia (Canada) were characterized using discriminant morphological traits, eight microsatellite loci, and mitochondrial DNA. Fifteen clonal genotypes were uncovered, all bearing the sameF. diaphanusmaternal haplotye. Each site harboured a different dominant clone along with several rarer clones that all appear to be of recent origin. Unexpectedly, highly introgressed sexually reproducing hybrids (0.25 > q > 0.75) were also detected. Sexual hybrids with maternal ascendance in either species were also found at three other sites in the Atlantic region. Based on a single meristic trait (scale counts), it is shown that asexual clones can be significantly more variable than populations of sexual parental species. Also, species are morphologically more alike when living in sympatry, suggesting that introgression may occur via sexual hybrids. Altogether, these results confirm and refine the available knowledge on this hybrid system, and indicate that hybridization is probably a more widespread phenomenon than suspected, with implications for the phenotypic variability of a widely used model species,F. heteroclitus.
Gene flow, effective population size and selection at major histocompatibility complex genes: brown trout in the Hardanger Fjord, Norway
Authors: HANSEN MICHAEL M. , SKAALA ØYSTEIN , JENSEN LASSE FAST , BEKKEVOLD DORTE , MENSBERG KAREN‐LISE D. 
Published: February 2007

AbstractBrown trout populations in the Hardanger Fjord, Norway, have declined drastically due to increased exposure to salmon lice from salmonid aquaculture. We studied contemporary samples from seven populations and historical samples (1972 and 1983) from the two largest populations, one of which has declined drastically whereas the other remains stable. We analysed 11 microsatellite loci, including one tightly linked to the UBA gene of the major histocompatibility class I complex (MHC) and another locus linked to the TAP2A gene, also associated with MHC. The results revealed asymmetric gene flow from the two largest populations to the other, smaller populations. This has important conservation implications, and we predict that possible future population recoveries will be mediated primarily by the remaining large population. Tests for selection suggested diversifying selection at UBA, whereas evidence was inconclusive for TAP2A. There was no evidence for temporally fluctuating selection. We assessed the distribution of adaptive divergence among populations. The results showed the most pronounced footprints of selection between the two largest populations subject to the least immigration. We suggest that asymmetric gene flow has an important influence on adaptive divergence and constrains local adaptive responses in the smaller populations. Even though UBA alleles may not affect salmon louse resistance, the results bear evidence of adaptive divergence among populations at immune system genes. This suggests that similar genetic differences could exist at salmon louse resistance loci, thus rendering it a realistic scenario that differential population declines could reflect differences in adaptive variation.
A comparison of AFLPs and microsatellites to identify the population structure of brown trout (Salmo trutta L.) populations from Hardangervidda, Norway
Authors: SØNSTEBØ J. H. , BORGSTRØM R. , HEUN M. 
Published: February 2007

AbstractA total of 495 fish from 11 Hardangervidda lakes were genotyped in order to compare amplified fragment length polymorphisms (AFLP) and microsatellites in terms of their capacity to infer population genetic structure. The 11 microsatellites used in this study gave a greater polymorphism information content and greater gene diversity, with an average of 14.8 alleles per locus, than the six AFLP primer combinations used. However, the AFLPs resulted in 178 polymorphic loci and a 3.1 times larger marker index (effective multiplex ratio multiplied with the gene diversity). Comparable population structuring, for example in terms of distinguishing fish from the different river systems, was obtained with both marker systems. An AFLP and microsatellite multilocus Bayesian assignment test with the structure program divided the fish into six groups largely concurrent with main branches on a population neighbour‐joining tree. Yet, the admixture status of individuals is mostly contradictory in the AFLP and the microsatellite analyses. The results are discussed concerning migration between lake populations.
Migration between continents: geographical structure and long‐distance gene flow in Porpidia flavicunda (lichen‐forming Ascomycota)
Authors: BUSCHBOM JUTTA 
Published: February 2007

AbstractHistorical and contemporary geographical distribution ranges with their associated gene flow patterns interact to produce the genetic diversity observed today. Often it is not possible to separate out the impacts of historical events, e.g. past fragmentation, and contemporary gene flow, e.g. long‐distance dispersal. Porpidia flavicunda is a lichen‐forming ascomycete occurring circumpolar in the boreal to arctic zones for which vegetation history suggests that its distribution pattern has stayed broadly the same over the past millennia. DNA‐sequence diversity in P. flavicunda can, thus, be expected to predominantly represent geographical population differentiation and its contemporary migration rates. The population sample consists of 110 specimens collected in Northern Québec, Baffin Island, Western Greenland and Northern Scandinavia. DNA‐sequence data sets of three nuclear gene fragments (LSU, RPB2 and β‐tubulin) were analysed for genetic diversity within, and differentiation between, geographical regions. Tests of population subdivision employing analyses of molecular variance and exact tests of haplotype frequency distributions showed significant structure between the geographical regions. However, the lack of fixed nucleotide polymorphisms and the wide sharing of identical haplotypes between geographical regions suggest recurrent long‐distance gene flow of propagules. Still, the means by which propagules are dispersed remain to be discovered. Inference of migration rates shows that in many cases a sufficiently high amount of migrants is exchanged between geographical regions to prevent drastic population differentiation through genetic drift. The observed haplotype distributions and migration rates point to a gene flow model of isolation by distance.
From the Apennines to the Alps: colonization genetics of the naturally expanding Italian wolf (Canis lupus) population
Authors: FABBRI ELENA , MIQUEL CHRISTIAN , LUCCHINI VITTORIO , SANTINI ALBERTO , CANIGLIA ROMOLO , DUCHAMP CHRISTOPHE , WEBER JEAN‐MARC , LEQUETTE BENOÎT , MARUCCO FRANCESCA , BOITANI LUIGI , FUMAGALLI LUCA , TABERLET PIERRE , RANDI ETTORE 
Published: February 2007

AbstractWolves in Italy strongly declined in the past and were confined south of the Alps since the turn of the last century, reduced in the 1970s to approximately 100 individuals surviving in two fragmented subpopulations in the central‐southern Apennines. The Italian wolves are presently expanding in the Apennines, and started to recolonize the western Alps in Italy, France and Switzerland about 16 years ago. In this study, we used a population genetic approach to elucidate some aspects of the wolf recolonization process. DNA extracted from 3068 tissue and scat samples collected in the Apennines (the source populations) and in the Alps (the colony), were genotyped at 12 microsatellite loci aiming to assess (i) the strength of the bottleneck and founder effects during the onset of colonization; (ii) the rates of gene flow between source and colony; and (iii) the minimum number of colonizers that are needed to explain the genetic variability observed in the colony. We identified a total of 435 distinct wolf genotypes, which showed that wolves in the Alps: (i) have significantly lower genetic diversity (heterozygosity, allelic richness, number of private alleles) than wolves in the Apennines; (ii) are genetically distinct using pairwiseFSTvalues, population assignment test and Bayesian clustering; (iii) are not in genetic equilibrium (significant bottleneck test). Spatial autocorrelations are significant among samples separated up toc. 230 km, roughly correspondent to the apparent gap in permanent wolf presence between the Alps and north Apennines. The estimated number of first‐generation migrants indicates that migration has been unidirectional and male‐biased, from the Apennines to the Alps, and that wolves in southern Italy did not contribute to the Alpine population. These results suggest that: (i) the Alps were colonized by a few long‐range migrating wolves originating in the north Apennine subpopulation; (ii) during the colonization process there has been a moderate bottleneck; and (iii) gene flow between sources and colonies was moderate (corresponding to 1.25–2.50 wolves per generation), despite high potential for dispersal. Bottleneck simulations showed that a total ofc. 8–16 effective founders are needed to explain the genetic diversity observed in the Alps. Levels of genetic diversity in the expanding Alpine wolf population, and the permanence of genetic structuring, will depend on the future rates of gene flow among distinct wolf subpopulation fragments.
The genetic structure of hawthorn‐infestingRhagoletis pomonellapopulations in Mexico: implications for sympatric host race formation
Authors: MICHEL ANDREW P. , RULL JUAN , ALUJA MARTIN , FEDER JEFFREY L. 
Published: February 2007

AbstractThe genetic origins of species may not all trace to the same time and place as the proximate cause(s) for population divergence. Moreover, inherent gene‐flow barriers separating populations may not all have evolved under the same geographical circumstances. These considerations have lead to a greater appreciation of the plurality of speciation: that one geographical mode for divergence may not always be sufficient to describe a speciation event. The apple maggot fly,Rhagoletis pomonella, a model system for sympatric speciation via host‐plant shifting, has been a surprising contributor to the concept of speciation mode plurality. Previous studies have suggested that past introgression of inversion polymorphism from a hawthorn‐fly population in the trans‐Mexican volcanic belt (EVTM) introduced diapause life‐history variation into a more northern fly population that subsequently contributed to sympatric host race formation and speciation in the United States (US). Here, we report results from a microsatellite survey implying (i) that volcanic activity in the eastern EVTM may have been responsible for the initial geographical isolation of the Mexican and northern hawthorn‐fly populationsc. 1.57 mya; and (ii) that flies in the Sierra Madre Oriental Mountains (SMO) likely served as a conduit for past gene flow from the EVTM into the US. Indeed, the microsatellite data suggest that the current US population may represent a range expansion from the northern SMO. We discuss the implications of these findings for sympatric race formation inRhagoletisand speciation theory.
Locating hybrid individuals in the red wolf(Canis rufus)experimental population area using a spatially targeted sampling strategy and faecal DNA genotyping
Authors: ADAMS JENNIFER R. , LUCASH CHRIS , SCHUTTE LESLIE , WAITS LISETTE P. 
Published: February 2007

AbstractHybridization with coyotes(Canis latrans)continues to threaten the recovery of endangered red wolves(Canis rufus)in North Carolina and requires the development of new strategies to detect and remove coyotes and hybrids. Here, we combine a spatially targeted faecal collection strategy with a previously published reference genotype data filtering method and a genetic test for coyote ancestry to screen portions of the red wolf experimental population area for the presence of nonred wolf canids. We also test the accuracy of our maximum‐likelihood assignment test for identifying hybrid individuals using eight microsatellite loci instead of the original 18 loci and compare its performance to the Bayesian approach implemented innewhybrids. We obtained faecal DNA genotypes for 89 samples, 73 of which were matched to 23 known individuals. The performance of two sampling strategies — comprehensive sweep and opportunistic spot‐check was evaluated. The opportunistic spot‐check sampling strategy required less effort than the comprehensive sweep sampling strategy but identified fewer individuals. Six hybrids or coyotes were detected and five of these individuals were subsequently captured and removed from the population. The accuracy and power of the genetic test for coyote ancestry is decreased when using eight loci; however, nonred wolf canids are identified with high frequency. This combination of molecular and traditional field‐based approaches has great potential for addressing the challenge of hybridization in other species and ecosystems.
Population differentiation and species cohesion in two closely related plants adapted to neotropical high‐altitude ‘inselbergs’,Alcantarea imperialisandAlcantarea geniculata(Bromeliaceae)
Authors: BARBARÁ T. , MARTINELLI G. , FAY M. F. , MAYO S. J. , LEXER C. 
Published: February 2007

AbstractIsolated granitic rock outcrops or ‘inselbergs’ may provide a window into the molecular ecology and genetics of continental radiations under simplified conditions, in analogy to the use of oceanic islands in studies of species radiations. Patterns of variability and gene flow in inselberg species have never been thoroughly evaluated in comparison to related taxa with more continuous distribution ranges, or to other species in the same kingdom in general. We use nuclear microsatellites to study population differentiation and gene flow in two diploid, perennial plants adapted to high‐altitude neotropical inselbergs,Alcantarea imperialisandAlcantarea geniculata(Bromeliaceae). Population differentiation is pronounced in both taxa, especially inA. imperialis. Gene flow in this species is considerably lower than expected from the literature on plants in general and Bromeliaceae in particular, and too low to prevent differentiation due to drift (Nem < 1), unless selection coefficients/effect sizes of favourable alleles are great enough to maintain species cohesion. Low gene flow inA. imperialisindicates that the ability of pollinating bats to promote gene exchange between inselbergs is smaller than previously assumed. Population subdivision in one inselberg population ofA. imperialisappears to be associated with the presence of two colour morphs that differ in the coloration of rosettes and bracts. Our results indicate a high potential for inselbergs as venues for studies of the molecular ecology and genetics of continental radiations, such as the one that gave rise to the extraordinary diversity of adaptive strategies and phenotypes seen in Bromeliaceae.
The Upregulation of Expressed Proteins in HepG2 Cells Transfected by the Recombinant Plasmid‐containing HBx Gene
Authors: He Y. , Yang F. , Wang F. , Song S.‐X. , Li D.‐A. , Guo Y.‐J. , Sun S.‐H. 
Published: February 2007

AbstractIt is known that the hepatitis B virus X protein (HBx) plays a crucial role in the pathogenesis of HCC, but the exact functions and molecular mechanisms of HBx in HCC are not well understood. In the present study, HepG2 cell lines were cultured and transfected with pEGFP‐N1 and pEGFP‐N1‐X. Twenty‐four hours after transfection, cells were harvested and total RNA was extracted using TRIzol® reagent. The expression of HBx in HepG2 cell line was assayed by real‐time polymerase chain reaction and was detected by Western blotting. Moreover, proteomic analysis was performed for the HepG2‐pEGFP‐X cells and HepG2‐pEGFP control cells. The combination of 2DE and MALDI‐TOF‐MS/MS revealed that SEC13L1 (SEC13‐like 1 isoform b), PA28 alpha (proteasome activator REG alpha), serine–threonine kinase receptor‐associated protein (STRAP) and nm23/nucleoside diphosphate kinase (NME) were upregulated in HepG2‐pEGFP‐X cells. STRAP is known to be a WD40 domain‐containing protein, which interacts with TβR‐I and TβR‐II and negatively regulates TGF‐β signalling, was also found increased in human cancers. NME is known to be involved in the regulation of cancer cell progression and metastasis. These results would help the understanding of how HBx maintains tumorigenicity and progression of HCC.
The Effect of Gene Gun‐delivered pGM‐CSF on the Immunopathology of the Vaccinated Skin
Authors: Matthews K. , Rhind S. M. , Gossner A. G. , Dalziel R. G. , Hopkins J. 
Published: February 2007

AbstractThe aim of this study was to investigate the skin immunopathology of gene gun‐delivered plasmid‐encoded granulocyte‐macrophage colony‐stimulating factor (pGM‐CSF) and hence explore the possible mechanisms of its adjuvant activity. Using sheep as the experimental model, expressible pGM‐CSF was administered to the epidermis and the dermal/epidermal junction and its effects on the skin were assessed by histopathology, immunohistology and quantitative RT‐PCR for a range of pro‐inflammatory and immune response‐polarizing cytokines. Both functional and non‐functional plasmids caused an acute inflammatory response with the infiltration of neutrophils and micro‐abscess formation; however, the response to pGM‐CSF was more severe and was also associated with the accumulation of eosinophils, immature (CD1b−/CD172a−) dendritic cells and B cells. In terms of cytokine expression, an early TNF‐α response was stimulated by gene gun delivery of plasmid‐associated gold beads, which coincided with an immediate infiltration of neutrophils. However, only pGM‐CSF triggered the short‐lived expression of GM‐CSF (peaking at 4 h) and significant long‐term increases in both TNF‐α and IL‐1β. pGM‐CSF did not affect the expression of the immune response‐polarizing cytokines, IL‐10 and IL‐12.
Comparative analysis of virulence determinants and mass spectral profiles of Finnish and Lithuanian endodontic Enterococcus faecalis isolates
Authors: Reynaud af Geijersstam A. , Culak R. , Molenaar L. , Chattaway M. , Røslie E. , Peciuliene V. , Haapasalo M. , Shah H. N. 
Published: February 2007

Introduction:  Putative virulence factors of Enterococcus faecalis have been proposed by several workers and, by analogy, these have been linked to strains of endodontic origin. However, their distribution within the cell population is unknown. In the present study, isolates were taken from the dental root canals of two defined human populations, Lithuanian and Finnish, and examined for a range of virulence properties. In addition, surface‐associated molecules and intracellular proteins were compared using matrix‐assisted laser desorption‐ionization/mass spectrometry (MALDI‐TOF‐MS) and ProteinChipTM capture/MS (SELDI‐TOF‐MS), respectively.Methods:  Twenty‐three Lithuanian and 35 Finnish dental root canal isolates were included. The esp, gelE, ace and efaA genes were detected by polymerase chain reaction, and cytolysin and gelatinase phenotypes were determined by hydrolysis of horse blood agar and gelatine agar, respectively. Protein extracts and surface‐associated molecules of whole cells were analysed by SELDI‐TOF‐MS and MALDI‐TOF‐MS, respectively.Results:  Presence of esp (n = 15), cytolysin (n = 9), ace (n = 55) and efaA (n = 58) was not statistically different in the two samples, whereas gelE and gelatinase production was detected more frequently in the Finnish material (chi‐squared, P < 0.01). Analysis of protein profiles by SELDI‐TOF‐MS showed clustering of cytolysin‐producing strains, whereas MALDI‐TOF‐MS generated profiles that clustered according to the samples’ origin and, furthermore, to atypical quinupristin–dalfopristin susceptibility.Conclusion:  A high prevalence of virulence factors was demonstrated in both population types. SELDI‐TOF‐MS and MALDI‐TOF‐MS proved useful in distinguishing between different E. faecalis phenotypes and they may be useful technologies for elucidating the eco‐distribution of E. faecalis in humans.
Lactobacillus plantarum for oral peptide delivery
Authors: Oh Y. , Varmanen P. , Han X. Y. , Bennett G. , Xu Z. , Lu T. , Palva A. 
Published: February 2007

Aims:  To evaluate strains of lactobacilli for their ability to persist and secrete heterologous protein in the oral cavity.Methods and results:  Four different strains of common oral lactobacilli, Lactobacillus brevis, Lactobacillus johnsonii, Lactobacillus murinus and Lactobacillus plantarum, were transformed with the plasmid pKTH2121, which contains a secretion cassette for beta‐lactamase. Lactobacilli isolated from the mouth of host mice were also transformed with pKTH2121 for later feeding. Lactococcus lactis, transformed with pKTH2121, was also fed to mice as a negative control. All transformed isolates were fed to C57Black mice in varying schedules. The number of transformed bacteria persisting in the mouth was reported as a percentage of total oral bacteria recovered by swabbing.Conclusions:  The transformed L. lactis, L. brevis, L. johnsonii, L. murinus, and the endogenous murine lactobacillus strain failed to persist in the mouth. Transformed L. plantarum, however, persisted in the mouth and comprised up to 25% of the total lactobacilli at 18 h and 10% at 24 h after feeding. L. plantarum recovered after feeding retained its ability to secrete beta‐lactamase into culture medium efficiently. Beta‐lactamase activity could be detected in oral secretions at 8 h after feedings. After repeated feedings, however, the L. plantarum containing pKTH2121 gradually lost its ability to persist after feedings. This experiment demonstrates that L. plantarum can transiently colonize the oral mucosa in large numbers, while continuously secreting foreign proteins, raising the possibility of using lactobacilli as a vector for delivery of oral mucosal peptides.