bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alendronate produces greater effects than raloxifene on bone density and bone turnover in postmenopausal women with low bone density: results of EFFECT (EFficacy of FOSAMAX® versus EVISTA®Comparison Trial) International1
Authors: Sambrook P. N. , Geusens P. , Ribot C. , Solimano J. A. , Ferrer‐Barriendos J. , Gaines K. , Verbruggen N. , Melton M. E. 
Published: December 2004

Abstract.Objectives.  Alendronate and raloxifene are antiresorptive agents with different mechanisms of action, each used to treat osteoporosis in postmenopausal women. This study was undertaken to compare the efficacy and tolerability of alendronate to raloxifene in postmenopausal women with low‐bone density.Design.  Randomized, double‐masked, double‐dummy multicentre international study.Setting.  Clinical trial centres in Europe, South America and Asia‐Pacific.Subjects.  A total of 487 postmenopausal women with low bone density, based on bone mineral density (BMD) of the lumbar spine or hip (T‐score ≤−2.0).Interventions.  Patients received either alendronate 70 mg once weekly and daily placebo identical to raloxifene or raloxifene 60 mg daily and weekly placebo identical to alendronate for 12 months.Main outcome measures.  Evaluations included BMD of the lumbar spine and hip and markers of bone turnover at 6 and 12 months and adverse event reporting.Results.  Alendronate demonstrated substantially greater increases in BMD than raloxifene at both lumbar spine and hip sites at 12 months. Lumbar spine BMD increased 4.8% with alendronate vs. 2.2% with raloxifene (P < 0.001). The increase in total hip BMD was 2.3% with alendronate vs. 0.8% with raloxifene (P < 0.001). Reductions in bone turnover were significantly larger with alendronate than raloxifene. Overall tolerability was similar, however, the proportion of patients reporting vasomotor events was significantly higher with raloxifene (9.5%) than with alendronate (3.7%, P = 0.010). The proportion of patients reporting gastrointestinal events was similar between groups.Conclusion.  In postmenopausal women with low bone density, improvements in BMD and markers of bone turnover were substantially greater during treatment with alendronate compared to raloxifene.
Estimating admixture proportions with microsatellites: comparison of methods based on simulated data
Authors: Choisy M. , Franck P. , Cornuet J.‐M. 
Published: December 2004

AbstractSeveral methods have been developed to estimate the parental contributions in the genetic pool of an admixed population. Some pair‐comparisons have been performed on real data but, to date, no systematic comparison of a large number of methods has been attempted. In this study, we performed a simulated data‐based comparison of six of the most cited methods in the literature of the last 20 years. Five of these methods use allele frequencies and differ in the statistical treatment of the data. The last one also considers the degree of molecular divergence by estimating the coalescence times. Comparisons are based on the frequency at which the method can be applied, the bias and the mean square error of the estimation, and the frequency at which the true value is within the confidence interval. Eventually, each method was applied to a real data set of variously introgressed honeybee populations. In optimal conditions (highly differentiated parental populations, recent hybridization event), all methods perform equally well. When conditions are not optimal, the methods perform differently, but no method is always better or worse than all others. Some guidelines are given for the choice of the method.
Using molecular markers with high mutation rates to obtain estimates of relative population size and to distinguish the effects of gene flow and mutation: a demonstration using data from endemic Mauritian skinks
Authors: Nichols R. A. , Freeman K. L. M. 
Published: December 2004

AbstractWe propose a method of analysing genetic data to obtain separate estimates of the size (Np) and migration rate (mp) for the sampled populations, without precise prior knowledge of mutation rates at each locus (µL). The effects of migration and mutation can be distinguished because high migration has the effect of reducing genetic differentiation across all loci, whereas a high mutation rate will only affect the locus in question. The method also takes account of any differences between the spectra of immigrant alleles and of new mutant alleles. If the genetic data come from a range of population sizes, and the loci have a range of mutation rates, it is possible to estimate the relative sizes of the different Np values, and likewise the mp and the µL. Microsatellite loci may also be particularly appropriate because loci with a high mutation rate can reach mutation–drift–migration equilibrium more quickly, and because the spectra of mutants arriving in a population can be particularly distinct from the immigrants. We demonstrate this principle using a microsatellite data set from Mauritian skinks. The method identifies low gene flow between a putative new species and populations of its sister species, whereas the differentiation of two other populations is attributed to small population size. These distinct interpretations were not readily apparent from conventional measures of genetic differentiation and gene diversity. When the method is evaluated using simulated data sets, it correctly distinguishes low gene flow from small population size. Loci that are not at mutation–migration–drift equilibrium can distort the parameter estimates slightly. We discuss strategies for detecting and overcoming this effect.
Population Graphs: the graph theoretic shape of genetic structure
Authors: Dyer Rodney J. , Nason John D. 
Published: December 2004

AbstractPatterns of intraspecific genetic variation result from interactions among both historical and contemporary evolutionary processes. Traditionally, population geneticists have used methods such as F‐statistics, pairwise isolation by distance models, spatial autocorrelation and coalescent models to analyse this variation and to gain insight about causal evolutionary processes. Here we introduce a novel approach (Population Graphs) that focuses on the analysis of marker‐based population genetic data within a graph theoretic framework. This method can be used to estimate traditional population genetic summary statistics, but its primary focus is on characterizing the complex topology resulting from historical and contemporary genetic interactions among populations. We introduce the application of Population Graphs by examining the range‐wide population genetic structure of a Sonoran Desert cactus (Lophocereus schottii). With this data set, we evaluate hypotheses regarding historical vicariance, isolation by distance, population‐level assignment and the importance of specific populations to species‐wide genetic connectivity. We close by discussing the applicability of Population Graphs for addressing a wide range of population genetic and phylogeographical problems.
Predominance of genetic monogamy by females in a hammerhead shark, Sphyrna tiburo: implications for shark conservation
Authors: Chapman Demian D. , Prodöhl Paulo A. , Gelsleichter James , Manire Charles A. , Shivji Mahmood S. 
Published: December 2004

AbstractThere is growing interest in the mating systems of sharks and their relatives (Class Chondrichthyes) because these ancient fishes occupy a key position in vertebrate phylogeny and are increasingly in need of conservation due to widespread overexploitation. Based on precious few genetic and field observational studies, current speculation is that polyandrous mating strategies and multiple paternity may be common in sharks as they are in most other vertebrates. Here, we test this hypothesis by examining the genetic mating system of the bonnethead shark, Sphyrna tiburo, using microsatellite DNA profiling of 22 litters (22 mothers, 188 embryos genotyped at four polymorphic loci) obtained from multiple locations along the west coast of Florida. Contrary to expectations based on the ability of female S. tiburo to store sperm, the social nature of this species and the 100% multiple paternity observed in two other coastal shark species, over 81% of sampled bonnethead females produced litters sired by a single male (i.e. genetic monogamy). When multiple paternity occurred in S. tiburo, there was an indication of increased incidence in larger mothers with bigger litters. Our data suggest that sharks may exhibit complex genetic mating systems with a high degree of interspecific variability, and as a result some species may be more susceptible to loss of genetic variation in the face of escalating fishing pressure. Based on these findings, we suggest that knowledge of elasmobranch mating systems should be an important component of conservation and management programmes for these heavily exploited species.
Influence of volcanic activity on the population genetic structure of Hawaiian Tetragnatha spiders: fragmentation, rapid population growth and the potential for accelerated evolution
Authors: Vandergast Amy G. , Gillespie Rosemary G. , Roderick George K. 
Published: December 2004

AbstractVolcanic activity on the island of Hawaii results in a cyclical pattern of habitat destruction and fragmentation by lava, followed by habitat regeneration on newly formed substrates. While this pattern has been hypothesized to promote the diversification of Hawaiian lineages, there have been few attempts to link geological processes to measurable changes in population structure. We investigated the genetic structure of three species of Hawaiian spiders in forests fragmented by a 150‐year‐old lava flow on Mauna Loa Volcano, island of Hawaii: Tetragnatha quasimodo (forest and lava flow generalist), T. anuenue and T. brevignatha (forest specialists). To estimate fragmentation effects on population subdivision in each species, we examined variation in mitochondrial and nuclear genomes (DNA sequences and allozymes, respectively). Population subdivision was higher for forest specialists than for the generalist in fragments separated by lava. Patterns of mtDNA sequence evolution also revealed that forest specialists have undergone rapid expansion, while the generalist has experienced more gradual population growth. Results confirm that patterns of neutral genetic variation reflect patterns of volcanic activity in some Tetragnatha species. Our study further suggests that population subdivision and expansion can occur across small spatial and temporal scales, which may facilitate the rapid spread of new character states, leading to speciation as hypothesized by H. L. Carson 30 years ago.
Spatio‐temporal variation in the genetic composition of wild populations of pearl oyster (Pinctada margaritifera cumingii) in French Polynesia following 10 years of juvenile translocation
Authors: Arnaud‐Haond S. , Vonau V. , Bonhomme F. , Boudry P. , Blanc F. , Prou J. , Seaman T. , Goyard E. 
Published: December 2004

AbstractThe genetic impact of the cultural practice of spat collection and translocation between genetically distinct stocks of black‐lipped pearl oyster, Pinctada margaritifera cumingii, was studied by comparing samples collected in the 1980s and 2000s from seven atolls in French Polynesia. An amova revealed homogenization of the previously genetically distinct wild stocks of Tuamotu‐Gambier and Society archipelagos (the indices of genetic differentiation among archipelagos and among populations within archipelagos, respectively, ΦCT and ΦST, decreased from 0.032* and 0.025*, respectively, to 0.006NS and 0.007NS). These results suggest high success of spontaneous reproduction in farms, probably due to the very high density of cultivated pearl oysters, and underline the importance of genetic monitoring of future hatchery produced stocks.
Limited phylogeographical structure across Eurasia in two red wood ant speciesFormica pratensisandF. lugubris(Hymenoptera, Formicidae)
Authors: Goropashnaya A. V. , Fedorov V. B. , Seifert B. , Pamilo P. 
Published: December 2004

AbstractThe phylogeography and demographic history of two closely related species of the red wood ant (Formica pratensisandF. lugubris) were examined across Eurasia. The phylogeny based on a 1.5‐kilobase mitochondrial DNA fragment, including the cytochromebgene and part of the ND6 gene, showed one phylogeographical division inF. pratensis.This division (0.7% of nucleotide divergence) suggests postglacial colonization of western Europe and of a wide area ranging from Sweden on the west to Lake Baikal on the east from separate forest refugia. In two localities, mitochondrial DNA has been transferred fromF. lugubristoF. pratensisand all the individuals ofF. pratensissampled from the Pyrenees had haplotypes clustering in thelugubrisclade. No phylogeographical divisions were detected inF. lugubris. Comparison of species‐wide phylogeography between the two sympatrically distributed species of ant demonstrates a difference in phylogeographical structure that implies different vicariant histories. However, over most of the species’ distribution ranges, similar signs of demographic expansion predating the last glaciation and the lack of phylogeographical structure were found in both the eastern phylogroup ofF. pratensisandF. lugubris.This finding is highly consistent with the results reported for all other boreal forest animal species studied to date in Eurasia. Contraction of the distribution range of each species to a single refugial area at different times during the late Pleistocene and a subsequent population expansion seem to be an explanation for the lack of phylogeographical structure across most of Eurasia in species that are ecologically associated with the boreal forest.
Population structure and phylogeography ofSolanum pimpinellifoliuminferred from a nuclear gene
Authors: Caicedo Ana Lucía , Schaal Barbara A. 
Published: December 2004

AbstractPhylogeographical studies are emerging as a powerful tool for understanding the population structure and evolution of wild relatives of crop species. Because of their value as genetic resources, there is great interest in exploring the distribution of variation in wild relatives of cultivated plants. In this study, we use sequence variation from the nuclear gene, fruit vacuolar invertase (Vac), to investigate the population history ofSolanum pimpinellifolium.Solanum pimpinellifoliumis a close relative of the cultivated tomato and has repeatedly served as a source of valuable traits for crop improvement. We sequenced the second intron of theVacgene in 129 individuals, representing 16 populations from the northern half of Peru. Patterns of haplotype sharing among populations indicate that there is isolation by distance. However, there is no congruence between the geographical distribution of haplotypes and their genealogical relationships. Levels of outcrossing decrease towards the southernmost populations, as previously observed in an allozyme study. The geographical pattern ofVacvariation supports a centre of origin in northern Peru forS. pimpinellifoliumand a gradual colonization along the Pacific coast. This implies that inbreeding populations are derived from outcrossing ones and that variation present at theVaclocus predates the spread ofS. pimpinellifolium. The expansion of cities and human agricultural activity in the habitat ofS. pimpinellifoliumcurrently pose a threat to the species.
Genetic structure of nest aggregations and drone congregations of the southeast Asian stingless beeTrigona collina
Authors: CAMERON E. C. , FRANCK P. , OLDROYD B. P. 
Published: December 2004

AbstractIn stingless bees, sex is determined by a single complementary sex‐determining locus. This method of sex determination imposes a severe cost of inbreeding because an egg fertilized by sperm carrying the same sex allele as the egg results in a sterile diploid male. To explore how reproductive strategies may be used to avoid inbreeding in stingless bees, we studied the genetic structure of a population of 27 colonies and three drone congregations ofTrigona collinain Chanthaburi, Thailand. The colonies were distributed across six nest aggregations, each aggregation located in the base of a different fig tree. Genetic analysis at eight microsatellite loci showed that colonies within aggregations were not related. Samples taken from three drone congregations showed that the males were drawn from a large number of colonies (estimated to be 132 different colonies in our largest swarm). No drone had a genotype indicating that it could have originated from the colony that it was directly outside. Combined, these results suggest that movements of drones and possibly movements of reproductive swarms among colony aggregations provide two mechanisms of inbreeding avoidance.
Phylogeography of a parasitoid wasp (Diaeretiella rapae): no evidence of host‐associated lineages
Authors: BAER C. F. , TRIPP D. W. , BJORKSTEN T. A. , ANTOLIN M. F. 
Published: December 2004

AbstractThe exceptional diversity of insects is often attributed to the effects of specialized relationships between insects and their hosts. Parasite–host interactions are influenced by current natural selection and dispersal, in addition to historical effects that may include past selection, vicariance, and random genetic drift. Both current and historical events can lead to reduced fitness on some hosts. If trade‐offs in fitness on alternate hosts are common, adaptation to one host can prevent adaptation to another, giving rise to genetic differentiation among host‐associated lineages. Previous studies ofDiaeretiella rapae(Hymenoptera: Aphidiidae), a parasitoid of aphids, have revealed additive genetic differences in performance between populations that parasitize different aphid host species. To determine whetherD. rapaepopulations collected from different aphid hosts have diverged into genetically independent lineages, we constructed a haplotype network based on sequence variation in mitochondrial DNA (mtDNA). We used single strand conformation polymorphism (SSCP) analysis to examine 2041 base pairs of mtDNA and to identify nucleotide sequences of 42 unique SSCP haplotypes. We found no association between mtDNA haplotypes and host species in either the ancestral range (Europe, Mediterranean region, Middle East, Asia) or part of the introduced range (western North America). Haplotypes likely to be ancestral were geographically widespread and found on both hosts, suggesting that the ability to use both hosts evolved prior to the diversification of the mtDNA. Ongoing gene flow appears to prevent the formation of host races.
Clonal structure and flowering traits of a bamboo [Phyllostachys pubescens(Mazel) Ohwi] stand grown from a simultaneous flowering as revealed by AFLP analysis
Authors: Isagi Y. , Shimada K. , Kushima H. , Tanaka N. , Nagao A. , Ishikawa T. , OnoDera H. , Watanabe S. 
Published: December 2004

AbstractAlthough many bamboo species are characterized by simultaneous flowering at long intervals of up to 120 years, few studies have revealed the length of the flowering interval for very‐long‐lived bamboo species by observing the whole life cycle of a single clone. The flowering interval ofPhyllostachys pubescenshad been determined to be 67 years by means of observation through the entire life cycle from 1912 to 1979. We observed and analysed the clonal structure and flowering traits of aP. pubescenscommunity which had regenerated from seed in 1930 and began to flower in 1997. Although this interval was again 67 years, flowering and nonflowering culms were mixed, and the flowering event lasted three years in the community. AFLP analysis of DNA samples showed distinct genets that originated from the previous flowering event and that each genet had its own flowering time. This is the first report to show that (i) different genets are mixed in a community of a large bamboo species with a leptomorphic rhizome system, and (ii) a community that originated from a single flowering event can have a range of flowering years.
Differential population structuring of two closely related fish species, the mackerel (Scomber scombrus) and the chub mackerel (Scomber japonicus), in the Mediterranean Sea
Authors: ZARDOYA R. , CASTILHO R. , GRANDE C. , FAVRE‐KREY L. , CAETANO S. , MARCATO S. , KREY G. , PATARNELLO T. 
Published: December 2004

AbstractPopulation genetic structures of the mackerel (Scomber scombrus) and chub mackerel (Scomber japonicus) were studied in the Mediterranean Sea. Fragments of 272 bp (S. scomber) and 387 bp (S. japonicus) of the 5′‐end of the mitochondrial control region were sequenced from spawning individuals collected off the coasts of Greece, Italy, Spain, and Portugal. High levels of mitochondrial control region haplotypic diversity (> 0.98) were found for both Scomber species. Nucleotide diversity was higher in the mackerel (0.022) than in the chub mackerel (0.017). Global FST values were also higher and significant in the mackerel (0.024, P < 0.0001) as opposed to the chub mackerel (0.003, P > 0.05). Molecular variance analyses showed differential genetic structuring for these two closely related species. There is extensive gene flow between Mediterranean Sea and Atlantic Ocean populations of chub mackerel, which are organized into a larger panmictic unit. In contrast, Mediterranean Sea populations of mackerel show some degree of genetic differentiation and are structured along an east–west axis. The analysed eastern Mediterranean Sea mackerel populations (Greece, Italy) are clearly separated from that of the western Mediterranean Sea (Barcelona), which forms a panmictic unit with eastern Atlantic Ocean populations. The genetic structures of both species showed asymmetric migration patterns and indicated population expansion.
Population biology of the invasive freshwater snail Physa acuta approached through genetic markers, ecological characterization and demography
Authors: BOUSSET L. , HENRY P‐Y. , SOURROUILLE P. , JARNE P. 
Published: December 2004

AbstractThe respective role of factors acting on population functioning can be inferred from a variety of approaches, including population genetics and demography. We here investigated the role of four of these factors (mating systems, population size, bottlenecks and migration) in the hermaphroditic freshwater snail Physa acuta. Twenty‐four populations were sampled either around Montpellier (local scale), or at the scale of France (global scale). At local scale, eight populations were sampled twice, before and after summer drying out. The genetic structure of these populations was studied using microsatellite loci. Populations were classified according to openness (ponds vs. rivers) and water regime (permanent vs. temporary) allowing predictions on genetic patterns (e.g. diversity within populations and differentiation). At local scale, progeny‐arrays analysis of the selfing rate was conducted, and size distributions of individuals were followed over two years. Results with regard to the four factors mentioned above were: (i) Estimates of population selfing rates derived from inbreeding coefficients were only slightly higher than those from progeny‐arrays. (ii) More variation was detected in rivers than in ponds, but no influence of water regime was detected. One reason might be that permanent populations are not going less often through low densities than those from temporary habitats at the time scale studied. (iii) There was limited evidence for genetic bottlenecks which is compatible with the fact that even marked reduction in water availability was not necessarily associated with demographic bottlenecks. More generally, bottlenecks reducing genetic variation probably occur at population foundation. (iv) Lower genetic differentiation was detected among rivers than among ponds which might be related to limitations on gene flow. Demographic and temporal genetic data further indicates that flooding in rivers is unlikely to induce marked gene flow explaining the strong genetic differentiation at short geographical scale in such habitats. Finally, the demographic data suggest that some populations are transitory and subject to recurrent recolonization, a pattern that was also detected through genetic data.