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Significant Differentiation (significant + differentiation)
Selected AbstractsSINE insertion polymorphism on the X chromosome differentiates Anopheles gambiae molecular formsINSECT MOLECULAR BIOLOGY, Issue 4 2005M. J. Barnes Abstract Polymorphic SINE insertions can be useful markers for assessing population structure and differentiation. Maque is a family of SINE elements which, based on bioinformatic analysis, was suggested to have been active recently in Anopheles gambiae, the major vector of malaria. Here, we report the development of polymorphic Maque insertions as population genetic markers in A. gambiae, and the use of these markers to better characterize divergence on the X chromosome between A. gambiae M and S molecular forms in populations from Burkina Faso and Mali. Our data are consistent with the recent activity of Maque. Phylogenetic analysis suggests that at least two recently active lineages may have a role in mediating genome evolution. We found differences in element insertion frequency and sequence between the M and S populations analysed. Significant differentiation was observed between these two groups across a 6 Mb region at the proximal (centromeric) end of the X chromosome. Locus-specific FST values ranged from 0.14 to 1.00 in this region, yet were not significantly different from zero in more distal locations on the X chromosome; the trend was consistent in populations from both geographical locales suggesting that differentiation is not due to local adaptation. Strong differentiation between M and S at the proximal end of the X chromosome, but not outside this region, suggests the action of selection counteracting limited gene flow between these taxa and supports their characterization as incipient species. [source] Genetic and morphometric differentiation among island populations of two Norops lizards (Reptilia: Sauria: Polychrotidae) on independently colonized islands of the Islas de Bahia (Honduras)JOURNAL OF BIOGEOGRAPHY, Issue 7 2007C. F. C. Klütsch Abstract Aim, Anole lizards (Reptilia: Sauria: Polychrotidae) display remarkable morphological and genetic differentiation between island populations. Morphological differences between islands are probably due to both adaptive (e.g. differential resource exploitation and intra- or interspecific competition) and non-adaptive differentiation in allopatry. Anoles are well known for their extreme diversity and rapid adaptive speciation on islands. The main aim of this study was to use tests of morphological and genetic differentiation to investigate the population structure and colonization history of islands of the Islas de Bahia, off the coast of Honduras. Location, Five populations of Norops bicaorum and Norops lemurinus were sampled, four from islands of the Islas de Bahia and one from the mainland of Honduras. Methods, Body size and weight differentiation were measured in order to test for significant differences between sexes and populations. In addition, individuals were genotyped using the amplified fragment length polymorphism technique. Bayesian model-based and assignment/exclusion methods were used to study genetic differentiation between island and mainland populations and to test colonization hypotheses. Results, Assignment tests suggested migration from the mainland to the Cayos Cochinos, and from there independently to both Utila and Roatán, whereas migration between Utila and Roatán was lacking. Migration from the mainland to Utila was inferred, but was much less frequent. Morphologically, individuals from Utila appeared to be significantly different in comparison with all other localities. Significant differentiation between males of Roatán and the mainland was found in body size, whereas no significant difference was detected between the mainland and the Cayos Cochinos. Main conclusions, Significant genetic and morphological differentiation was found among populations. A stepping-stone model for colonization, in combination with an independent migration to Utila and Roatán, was suggested by assignment tests and was compatible with the observed morphological differentiation. [source] Divergent host plant adaptation drives the evolution of sexual isolation in the grasshopper Hesperotettix viridis (Orthoptera: Acrididae) in the absence of reinforcementBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2010TONY GRACE Early stages of lineage divergence in insect herbivores are often related to shifts in host plant use and divergence in mating capabilities, which may lead to sexual isolation of populations of herbivorous insects. We examined host preferences, degree of differentiation in mate choice, and divergence in cuticular morphology using near-infrared spectroscopy in the grasshopper Hesperotettix viridis aiming to understand lineage divergence. In Kansas (USA), H. viridis is an oligophagous species feeding on Gutierrezia and Solidago host species. To identify incipient mechanisms of lineage divergence and isolation, we compared host choice, mate choice, and phenotypic divergence among natural grasshopper populations in zones of contact with populations encountering only one of the host species. A significant host-based preference from the two host groups was detected in host-paired feeding preference studies. No-choice mate selection experiments revealed a preference for individuals collected from the same host species independent of geographic location, and little mating was observed between individuals collected from different host species. Female mate choice tests between males from the two host species resulted in 100% fidelity with respect to host use. Significant differentiation in colour and cuticular composition of individuals from different host plants was observed, which correlated positively with host choice and mate choice. No evidence for reinforcement in the zone of contact was detected, suggesting that divergent selection for host plant use promotes sexual isolation in this species. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 866,878. [source] Genetic differentiation among the Maculinea species (Lepidoptera: Lycaenidae) in eastern Central EuropeBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2007KATALIN PECSENYE The present study aimed to analyse the level of genetic variation in the eastern Central European (Slovenia, Hungary, and Romania/Transylvania) populations of the Large Blues (Maculinea) to analyse the pattern of differentiation both between and within the species. One objective was to compare the level of differentiation between the two disputed species (Maculinea alcon and Maculinea rebeli) with that among the other species. Imagos were collected from 23 localities in eastern Central Europe in 2002. Enzyme polymorphism was analysed using polyacrylamide gel electrophoresis. Fourteen enzyme loci were studied in all samples. In the analysis of the data, F -statistics and Nei's genetic distances were calculated and a dendrogram (unweighted pair group method with arithmetic mean) was constructed on the basis of the distance matrix. A multivariate analysis of variance was performed to study the pattern of genetic differentiation among the samples. Principal component analysis analysis was also carried out using the allele frequency data of the samples. Our results indicated that the large blues are generally less polymorphic than other European lycaenid butterflies studied. At the same time, the level of genetic differentiation was high, even among local populations within the species. A low level of genetic variation within the populations coupled with strong differentiation among them implies the effect of genetic drift. Strong genetic differentiation of four Maculinea species (M. alcon, Maculinea teleius, Maculinea nausithous, and Maculinea arion) was confirmed. Significant differentiation was not found between M. alcon and M. rebeli. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 91, 11,21. [source] A REAPPRAISAL OF THE OVERLAP OF VIOLENT OFFENDERS AND VICTIMS,CRIMINOLOGY, Issue 4 2008CHRISTOPHER J. SCHRECK Because research shows a close association between offending and victimization, recent work has argued that theories that account for crime should explain victimization as well. The current study uses a new approach to examine the extent of the overlap between offenders who commit violent crime and victims of violence to determine whether it is worthwhile to pursue separate theories to account for these phenomena. Specifically, we take the statistical approach that Osgood and Schreck (2007) developed for analyzing specialization in violent versus property offending and apply it to analyzing tendencies to gravitate toward violent offending versus victimization. In doing so, we treat the differentiation into victim and offender roles as an individual-level latent variable while controlling for confounding between the likelihood that individuals will take either role in violent acts and their overall numbers of encounters with violence (as either offender or victim). Our purpose is to examine 1) whether significant differentiation can be observed between the tendency to be an offender versus the tendency to be a victim, 2) whether any such differential tendency is stable over time, and 3) if it is possible to predict whether individuals will tend toward violent offending versus victimization. Using two waves of data from the National Longitudinal Study of Adolescent Health to explore these objectives, we find significant and stable levels of differentiation between offenders and victims. Moreover, this differentiation is predictable with explanatory variables. [source] Do dams increase genetic diversity in brown trout (Salmo trutta)?ECOLOGY OF FRESHWATER FISH, Issue 4 2006Microgeographic differentiation in a fragmented river Abstract , Local genetic differentiation may potentially arise in recently fragmented populations. Brown trout is a polytypic species exhibiting substantial genetic differentiation, which may evolve in few generations. Movement (semi-)barriers in rivers may cause fragmentation, isolation and genetic differentiation in fish. In the Måna River (28 km) flowing from the alpine Lake Møsvatn to the boreal Lake Tinnsjø, construction of four hydropower dams during the period 1906,1957 have fragmented the previously (since last Ice Age) continuous wild resident brown trout population. Samples from the two lakes (N = 40) and six sites in the river (N = 30) isolated at different times were analysed at nine microsatellite loci. All populations showed substantial genetic variation (mean number of alleles per locus 5.3,8.9, observed heterozygosity 0.57,0.65 per population, overall Fst = 0.032). Pairwise multilocus Fst estimates indicated no significant differentiation between populations in the two lakes, and no or little differentiation in the lower river (Fst = 0.0035,0.0091). The microgeographic differentiation among wild resident trout at these sites was less than expected based on similar previous studies. However, results from the upper river, in particular the site immediately below the Lake Møsvatn outlet and dam, indicated isolation (Fst > 0.035). Calculation of genetic distances and assignment tests corroborated these results, as did a significant correlation between years of isolation (since dam construction) and Fst. The population structuring is most likely a result of fragmentation by dams, which has increased overall genetic diversity. This increased local differentiation may be caused by natural selection, but more likely by genetic drift in small, recently fragmented populations. Increased local genetic diversity by genetic drift does not justify conservation measures aiming at preserving genetic diversity. [source] Induction of endogenous neural precursors in mouse models of spinal cord injury and diseaseEUROPEAN JOURNAL OF NEUROLOGY, Issue 8 2005M. F. Azari Adult neural precursor cells (NPCs) in the mammalian central nervous system (CNS) have been demonstrated to be responsive to conditions of injury and disease. Here we investigated the response of NPCs in mouse models of spinal cord disease [motor neuron disease (MND)] with and without sciatic nerve axotomy, and spinal cord injury (SCI). We found that neither axotomy, nor MND alone brought about a response by Nestin-positive NPCs. However, the combination of the two resulted in mobilization of NPCs in the spinal cord. We also found that there was an increase in the number of NPCs following SCI which was further enhanced by systemic administration of the neuregulatory cytokine, leukaemia inhibitory factor (LIF). NPCs were demonstrated to differentiate into astrocytes in axotomized MND mice. However, significant differentiation into the various neural cell phenotypes was not demonstrated at 1 or 2 weeks following SCI. These data suggest that factors inherent to injury mechanisms are required for induction of an NPC response in the mammalian spinal cord. [source] Genetic variability in Irish populations of the invasive zebra mussel, Dreissena polymorpha: discordant estimates of population differentiation from allozymes and microsatellitesFRESHWATER BIOLOGY, Issue 7 2008ELIZABETH GOSLING Summary 1. The recent arrival and explosive spread of the zebra mussel, Dreissena polymorpha (Pallas), in Ireland provided a rare opportunity to study the population genetics of an invasive species. 2. Eight polymorphic allozyme loci (ACO-1, ACO-2, EST-D, GPI, IDH-2, MDH, OPDH and PGM) were used to investigate genetic diversity and population structure in five Irish populations, and the results were compared with those from a previous microsatellite study on the same samples. 3. The mean number of alleles per locus (2.7 ± 0.1) was similar to the mean for the same loci in European populations, suggesting that Irish founder populations were large and/or multiple colonization events took place after foundation. A deficiency of heterozygotes was observed in all populations, but was uneven across loci. 4. Pairwise comparisons, using Fisher's exact tests and FST values, revealed significant genetic differentiation among populations. The overall multilocus FST estimate was 0.118 ± 0.045, which contrasted with an estimate of 0.015 ± 0.007 from five microsatellite loci on the same samples in a previous study. 5. Assuming that microsatellites can be used as a neutral baseline, the discordant results from allozymes and microsatellites suggest that selection may be acting on some allozyme loci, specifically ACO-1, ACO-2, IDH-2 and MDH, which contributed most to the significant differentiation between samples. [source] Phylogeographical structure in the coastal species Senecio rodriguezii (Asteraceae), a narrowly distributed endemic Mediterranean plantJOURNAL OF BIOGEOGRAPHY, Issue 7 2009Arántzazu Molins Abstract Aim, Our goals were (1) to assess the levels of chloroplast DNA variation in a narrowly distributed plant restricted to continental islands, (2) to ascertain whether a phylogeographical structure is present in plants restricted to coastal linear systems, and (3) to interpret the results in the light of the known palaeogeography of these islands. Location, The Eastern Balearic Islands (Majorca and Minorca) in the Western Mediterranean Basin. Methods, Sampling included 134 individuals from 28 populations of Senecio rodriguezii covering the entire range of the species. Sequences of the chloroplast genome (trnT,trnL spacer) were obtained and parameters of population genetic diversity and substructure were determined (hsht, Gst). The geographical structure of genetic variation was assessed by an analysis of molecular variance (AMOVA). Additionally, a spatial AMOVA (SAMOVA) was used to identify groups of populations that were geographically homogeneous and maximally differentiated from each other. Finally, a pattern of isolation by distance was assessed by testing the correlation between the matrix of pairwise ,ST values and the matrix of geographical distances between pairs of populations using a Mantel test. Results, Seven haplotypes were detected in S. rodriguezii. Only two of them were shared between islands; all of the others were restricted to Majorca (two) or Minorca (three). Overall, we found high levels of genetic diversity and significant geographical structuring of cpDNA markers. Most of the variation detected can be attributed to differences among populations (84.6%), but there was also a significant differentiation between the islands. Main conclusions, Our results support the view that the Balearic Islands constitute a reservoir of genetic diversity, not only for widespread Mediterranean taxa, but also for endemic ones. The intraspecific genetic structure found in S. rodriguezii suggests that its population history was dominated by both expansion and contraction events. This has resulted in a species that is highly structured genetically, showing very few shared haplotypes between islands, and a high number of haplotypes restricted to small geographical areas within the islands. Changes in habitat availability and dynamic processes of population fragmentation and connectivity due to repeated cycles of sea-level changes during the Quaternary are the possible underlying factors that have shaped the cpDNA pool of this endemic species on a regional scale. [source] Marine biogeographical structure in two highly dispersive gastropods: implications for trans-Tasman dispersalJOURNAL OF BIOGEOGRAPHY, Issue 4 2007Jonathan M. Waters Abstract Aim, Recent genetic and ecological studies of marine invertebrate species with planktotrophic larvae have inferred high rates of gene flow across wide oceanic barriers. We therefore aim to test for the genetic signature of long-distance dispersal in two widespread and abundant marine gastropod taxa. Location, The intertidal and shallow subtidal zones of southern Australia and New Zealand (NZ), which house similar marine invertebrate assemblages despite being separated by the 2000-km-wide Tasman Sea. Methods, We used mtDNA cytochrome oxidase I gene sequence analysis of two gastropod genera exhibiting trans-Tasman distributions, namely Austrolittorina (Littorinidae) (139 specimens; 28 localities) and Scutus (Fissurellidae) (154 specimens; 32 localities). The cool-temperate Australian (A. unifasciata; S. antipodes) and NZ (A. antipodum; S. breviculus) taxa within each genus are morphologically similar but of uncertain taxonomic status. Results, The mtDNA analyses indicate major trans-Tasman genetic discontinuities for both gastropod genera, with no evidence of recent or ongoing intercontinental gene flow. Although both Scutus and Austrolittorina show significant east,west structure within southern Australia , consistent with recent studies of regional marine phylogeography , neither taxon exhibits significant differentiation within NZ. Main conclusions, Morphologically conserved but biogeographically disjunct gastropod populations may exhibit striking phylogeographic discontinuities, even when dispersal abilities appear to be high. On the basis of these data we reject recent calls for the synonymy of NZ and Australian lineages. [source] Dispersal and gene flow of Populus nigra (Salicaceae) along a dynamic river systemJOURNAL OF ECOLOGY, Issue 3 2003Eric Imbert Summary 1,We used genetic markers to study gene flow of the riparian pioneer tree species Populus nigra along the Drôme river (France). This dioecious species is supposed to have more efficient dispersal mechanisms for pollen (wind) and seeds (wind and water) than other trees. 2,Seedlings belonging to the same reproduction/migration event were sampled in 22 riparian forest fragments along the river and their genetic diversity assessed through six nuclear microsatellites. 3,We found a high level of diversity and significant differentiation among populations. The significant isolation by distance allowed us to reject the infinite island model of migration. 4,Gene flow parameters were higher in the upper, mountainous part than in the alluvial plain downstream. There was no accumulation of diversity downstream, indicating migration rates were symmetrical upstream and downstream. This was confirmed by computing individual migration parameters between adjacent populations. 5,The results are discussed with regard to the dispersal mechanisms of seeds and pollen. The discrepancy between potential gene flow and effective gene flow is interpreted as an effect of fragmentation, due to the alteration of the natural dynamics of the riparian ecosystem rather than to physical barriers. [source] Distinguishing between two sympatric Acanthopagrus species from Dapeng Bay, Taiwan, using morphometric and genetic charactersJOURNAL OF FISH BIOLOGY, Issue 2 2009M. C. Tseng Morphometric and genetic data were used to compare two sympatric and morphologically similar species, Acanthopagrus berda and Acanthopagrus taiwanensis, in Dapeng Bay, South-western Taiwan. A principle component analysis of morphological data indicated a distinction between the two species, with pectoral fin length and eye diameter accounting for 32·27% of the variation. Interspecific sequence divergence, based on mtDNA cytochrome b (0·118 ± 0·01), was larger than intraspecific divergences between haplotypes (0·007 for A. taiwanensis and 0·003 for A. berda). Individuals of the two species clustered into different groups in three phylogenetic trees with 100% bootstrap support. The mean observed heterozygosity for eight microsatellite loci was 0·471 ± 0·202 for A. taiwanensis and 0·637 ± 0·145 for A. berda. Nei's unbiased measure of interspecific genetic distance (DS) was 1·334. FST (0·134) and RST (0·404) values indicated significant differentiation between species. An unrooted neighbour-joining tree was constructed by allele-sharing distances and the factorial correspondence analysis split all specimens into two distinct clusters. The results of morphometric, mtDNA and microsatellite analyses indicated the presence of two species, A. taiwanensis and A. berda. [source] Two Genetically Distinct Populations of Colletotrichum gloeosporioides Penz.JOURNAL OF PHYTOPATHOLOGY, Issue 3 2005Causing Anthracnose Disease of Yam (Dioscorea spp.) Abstract Variation within Colletotrichum gloeosporioides, the causal agent of yam anthracnose disease, is still poorly defined and this hinders breeding for resistance. Two morphotypes of C. gloeosporioides, designated slow-growing grey (SGG) and fast-growing salmon (FGS), are associated with anthracnose disease of yam in Nigeria. The morphotypes are distinguishable based on colony and conidial morphology, growth rate, virulence, as well as vegetative compatibility, but molecular differentiation of SGG and FGS strains is needed to facilitate epidemiological studies. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified small subunit (18S) rDNA fragments, and microsatellite-primed PCR (MP-PCR) genomic fingerprinting were employed to provide a basis for molecular differentiation of the morphotypes. DGGE analysis revealed patterns that clearly differentiated isolates of the aggressive defoliating SGG from the moderately virulent non-defoliating FGS strains. Genetic analysis based on 52 MP-PCR markers revealed highly significant differentiation between the SGG and FGS populations on yam (GST = 0.22; Nei's genetic identity = 0.85; , = 0.28, P < 0.001), indicating that the SGG and FGS morphotypes represent genetically differentiated populations. The results of the molecular typing using DGGE and MP-PCR analyses were consistent with the disease phenotype caused by the two morphotypes. Consequently, these molecular techniques might be used, at least partly, to replace time-consuming virulence studies on yam. [source] Determination of radix ginseng volatile oils at different ages by comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometryJOURNAL OF SEPARATION SCIENCE, JSS, Issue 19 2008Yaqiong Qiu Abstract Comprehensive 2-D GC (GC×GC) coupled with TOF MS or flame ionization detector (FID) was employed to characterize and quantify the chemical composition of volatile oil in the radixes of Panax ginseng C. A. Mey. (ginseng) at different ages. Thirty-six terpenoids were tentatively identified based on the MS library search and retention index in a ginseng sample at the age of 3 years. An obvious group-type separation was obtained in the GC×GC-TOF MS chromatogram. The data collected by GC×GC-FID were processed using a principal component analysis (PCA) method to classify the samples at different ages. The compounds responsible for the significant differentiation among samples were defined. It was found that the relative abundances of ,-cadinol, ,-bisabolol, thujopsene, and n -hexadecanoic acid significantly rise with the increase in age. [source] Evolutionary assessment of Artemia tibetiana (Crustacea, Anostraca) based on morphometry and 16S rRNA RFLP analysisJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2005A. D. Baxevanis Abstract Over the last few years, molecular-based assays in the genus Artemia have considerably enriched prior systematic assessments based on morphometry. For the first time, morphometric and 16S rRNA PCR-RFLP analyses on all type-locality bisexual species of the genus have been employed here. Emphasis was put on the Asian species (Artemia urmiana, A. tibetiana, A. sinica) where patterns of divergence and reproductive isolation are rather discrete, and especially on A. tibetiana for which recent reports have questioned its specific status. Discriminant analysis of morphometric characters has shown significant differentiation among species. Classification scores were 99.4 and 100% for males and females, respectively. Mitochondrial DNA RFLP patterns have given indications for lower, albeit similar patterns of differentiation compared with those obtained by morphometry. Artemia tibetiana and A. urmiana are mitochondrially indistinguishable which is suggestive of recent ancestry. Our data, in conjunction with past evidence, are supportive of a significant amount of divergence between A. tibetiana and A. sinica. Morphometric and molecular assays can be reciprocally informative provided theory and patterns of speciation are incorporated into systematic assessments. Résumé Ces dernières années, les outils moléculaires utilisés dans l'étude du genre Artemia ont considèrablement enrichi les analyses systématiques antérieures basées sur la morphométrie. Pour la première fois, des analyses morphométriques et des analyses PCR-RFLP de l'ARN ribosomique 16S ont été effectuées pour toutes les espèces amphigoniques d'Artemia venant des localités types. Dans cette étude, nous nous sommes concentrés sur les espèces asiatiques (A. urmiana, A. tibetiana, A. sinica), qui présentent des traits de divergence et un isolement reproductif assez singuliers, et tout particulièrement sur l'A. tibetiana dont le statut d'espèce à part entière a été mis en doute dans de récentes études. Une analyse discriminante des caractéristiques morphométriques a révélé une différenciation importante parmi les espèces. Pour les mâles et les femelles, les scores de classification étaient respectivement de 99,4% et 100%. Les profils RFLP de l'ADN mitochondrial ont montré une différenciation similaire à celle observée grâce à l'analyse morphométrique. L'ADN mitochondrial de l'A. tibetiana est indifférenciable de celui de l'A. urmiana, ce qui suggère que ces deux espèces ont récemment divergé. Nos données, combinées à celles recueillies par le passé, indiquent une grande divergence entre l'A. tibetiana et l'A. sinica. Les analyses morphométriques et moléculaires peuvent se compléter à condition de tenir compte de la théorie de la spéciation et des modèles de spéciation durant les analyses systématiques. [source] Inferring the evolutionary history of Drosophila americana and Drosophila novamexicana using a multilocus approach and the influence of chromosomal rearrangements in single gene analysesMOLECULAR ECOLOGY, Issue 12 2008RAMIRO MORALES-HOJAS Abstract The evolutionary history of closely related organisms can prove sometimes difficult to infer. Hybridization and incomplete lineage sorting are the main concerns; however, genome rearrangements can also influence the outcome of analyses based on nuclear sequences. In the present study, DNA sequences from 12 nuclear genes, for which the approximate chromosomal locations are known, have been used to estimate the evolutionary history of two forms of Drosophila americana (Drosophila americana americana and Drosophila americana texana) and Drosophila novamexicana (virilis group of species). The phylogenetic analysis of the combined data set resulted in a phylogeny showing reciprocal monophyly for D. novamexicana and D. americana. Single gene analyses, however, resulted in incongruent phylogenies influenced by chromosomal rearrangements. Genetic differentiation estimates indicated a significant differentiation between the two species for all genes. Within D. americana, however, there is no evidence for differentiation between the chromosomal forms except at genes located near the X/4 fusion and Xc inversion breakpoint. Thus, the specific status of D. americana and D. novamexicana is confirmed, but there is no overall evidence for genetic differentiation between D. a. americana and D. a. texana, not supporting a subspecific status. Based on levels of allele and nucleotide diversity found in the strains used, it is proposed that D. americana has had a stable, large population during the recent past while D. novamexicana has speciated from a peripheral southwestern population having had an ancestral small effective population size. The influence of chromosomal rearrangements in single gene analyses is also examined. [source] Social kin associations and genetic structuring of striped dolphin populations (Stenella coeruleoalba) in the Mediterranean SeaMOLECULAR ECOLOGY, Issue 14 2007STEFANIA GASPARI Abstract We investigated hierarchical patterns of genetic subdivision, and assessed kinship within and between social groups of striped dolphins (Stenella coeruleoalba) in the Tyrrhenian Sea. A total of 165 samples were analysed at eight microsatellite DNA loci, including outgroup samples from the Adriatic, Scotland and Spain for population-level comparisons. We found population genetic structure within the Mediterranean basin, including small but significant differentiation between the Adriatic and Tyrrhenian Seas (FST = 0.0047, P = 0.008), and between putative ,inshore' and ,offshore' (FST = 0.0217, P = 0.005) populations in the Tyrrhenian Sea. Assessment of kinship within and among 12 association groups showed higher average kinship for females within than between groups, and smaller groups showed higher average kinship. Comparisons of relatedness for both sexes showed a significant difference between males and females, with females more likely to associate with adult kin. Together these data emphasize the importance of the social cohesion of kin in small groups to the structuring of striped dolphin populations in this environment. [source] Linked vs. unlinked markers: multilocus microsatellite haplotype-sharing as a tool to estimate gene flow and introgressionMOLECULAR ECOLOGY, Issue 2 2007WIM J. M. KOOPMAN Abstract We have explored the use of multilocus microsatellite haplotypes to study introgression from cultivated (Malus domestica) into wild apple (Malus sylvestris), and to study gene flow among remnant populations of M. sylvestris. A haplotype consisted of alleles at microsatellite loci along one chromosome. As destruction of haplotypes through recombination occurs much faster than loss of alleles due to genetic drift, the lifespan of a multilocus haplotype is much shorter than that of the underlying alleles. When different populations share the same haplotype, this may indicate recent gene flow between populations. Similarly, haplotypes shared between two species would be a strong signal for introgression. As the expected lifespan of a haplotype depends on the strength of the linkage, the length [in centiMorgans (cM)] of the haplotype shared contains information on the number of generations passed. This application of shared haplotypes is distinct from using haplotype-sharing to detect association between markers and a certain trait. We inferred haplotypes for four to eight microsatellite loci on Linkage Group 10 of apple from genotype data using the program phase, and then identified those haplotypes shared between populations and species. Compared with a Bayesian analysis of unlinked microsatellite loci using the program structure, haplotype-sharing detected a partially different set of putative hybrids. Cultivated haplotypes present in M. sylvestris were short (< 1.5 cM), indicating that introgression had taken place many generations ago, except for two Belgian plants that contained a haplotype of 47.1 cM, indicating recent introgression. In the estimation of gene flow, FST based on unlinked loci indicated small (0.032,0.058) but statistically significant differentiation between some populations only. However, various M. sylvestris haplotypes were shared in nearly all pairwise comparisons of populations, and their length indicated recent gene flow. Hence, all Dutch populations should be considered as one conservation unit. The added value of using sharing of multilocus microsatellite haplotypes as a source of population genetic information is discussed. [source] Nuclear and mitochondrial markers reveal distinctiveness of a small population of bottlenose whales (Hyperoodon ampullatus) in the western North AtlanticMOLECULAR ECOLOGY, Issue 11 2006MEREL L. DALEBOUT Abstract Small populations at the edge of a species' distribution can represent evolutionary relics left behind after range contractions due to climate change or human exploitation. The distinctiveness and genetic diversity of a small population of bottlenose whales in the Gully, a submarine canyon off Nova Scotia, was quantified by comparison to other North Atlantic populations using 10 microsatellites and mitrochondrial DNA (mtDNA) control region sequences (434 bp). Both markers confirmed the distinctiveness of the Gully (n = 34) from the next nearest population, off Labrador (n = 127; microsatellites ,FST= 0.0243, P < 0.0001; mtDNA ,,ST = 0.0456, P < 0.05). Maximum likelihood microsatellite estimates suggest that less than two individuals per generation move between these areas, refuting the hypothesis of population links through seasonal migration. Both males and females appear to be philopatric, based on significant differentiation at both genomes and similar levels of structuring among the sexes for microsatellites. mtDNA diversity was very low in all populations (h = 0.51, , = 0.14%), a pattern which may be due to selective sweeps associated with this species' extreme deep-diving ecology. Whaling had a substantial impact on bottlenose whale abundance, with over 65 000 animals killed before the hunt ceased in the early 1970s. Genetic diversity was similar among all populations, however, and no signal for bottlenecks was detected, suggesting that the Gully is not a relic of a historically wider distribution. Instead, this unique ecosystem appears to have long provided a stable year-round habitat for a distinct population of bottlenose whales. [source] The ruddy duck Oxyura jamaicensis in Europe: natural colonization or human introduction?MOLECULAR ECOLOGY, Issue 6 2006VIOLETA MUÑOZ-FUENTES Abstract Native to North America, ruddy ducks Oxyura jamaicensis now occur in 21 countries in the western Palaearctic (including Iceland) and their expanding population threatens the native white-headed duck, Oxyura leucocephala, through hybridization and possibly competition for food and nest sites. We used mitochondrial DNA sequences and nuclear microsatellites to test whether the European ruddy duck population is descended solely from the captive population in the UK, which traces to seven individuals imported from the USA in 1948, or, alternatively, has been augmented by natural dispersal of birds from North America. Limited genetic diversity in the European population is consistent with a founder population as small as seven birds. In addition, shifts in allele frequencies at several loci, presumably due to genetic drift in the founding population, result in significant differentiation between the European and North American populations. Despite the recent separation of these populations, almost all individuals could be unambiguously assigned based on their composite genotypes, to one of two distinct populations, one comprising all of the European ruddy ducks we sampled (including those from Iceland and captive birds in the UK) and the other comprising all North American samples. Our results confirm that the European ruddy duck population is likely to derive solely from the captive population in the UK and we find no evidence of recent arrivals from North America or of admixture between ruddy ducks from Europe and North America. [source] Landscape scale genetic effects of habitat fragmentation on a high gene flow species: Speyeria idalia (Nymphalidae)MOLECULAR ECOLOGY, Issue 1 2003Barry L. Williams Abstract Detection of the genetic effects of recent habitat fragmentation in natural populations can be a difficult task, especially for high gene flow species. Previous analyses of mitochondrial DNA data from across the current range of Speyeria idalia indicated that the species exhibited high levels of gene flow among populations, with the exception of an isolated population in the eastern portion of its range. However, some populations are found on isolated habitat patches, which were recently separated from one another by large expanses of uninhabitable terrain, in the form of row crop agriculture. The goal of this study was to compare levels of genetic differentiation and diversity among populations found in relatively continuous habitat to populations in both recently and historically isolated habitat. Four microsatellite loci were used to genotype over 300 individuals from five populations in continuous habitat, five populations in recently fragmented habitat, and one historically isolated population. Results from the historically isolated population were concordant with previous analyses and suggest significant differentiation. Also, microsatellite data were consistent with the genetic effects of habitat fragmentation for the recently isolated populations, in the form of increased differentiation and decreased genetic diversity when compared to nonfragmented populations. These results suggest that given the appropriate control populations, microsatellite markers can be used to detect the effects of recent habitat fragmentation in natural populations, even at a large geographical scale in high gene flow species. [source] Fitness and genetic variation of Viola calaminaria, an endemic metallophyte: implications of population structure and historyPLANT BIOLOGY, Issue 6 2008J.-P. Bizoux Abstract We investigated variations in genetic diversity and plant fitness in a rare endemic metallophyte of calamine soils, Viola calaminaria, in relation to population size, population connectivity and population history in order to evaluate and discuss potential conservation strategies for the species. Mean population genetic diversity (Hs = 0.25) of V. calaminaria was similar to endemic non-metallophyte taxa. Twenty-one per cent of the genetic variation was partitioned among populations and a low (9%) but significant differentiation was found among geographical regions. Our results did not support the hypothesis that the acquisition of metal tolerance may result in reduced genetic diversity, and suggested that strict metallophytes do not exhibit higher inter-population differentiation resulting from scattered habitats. There were no relationships between population genetic diversity and population size. Significant correlations were found between plant fitness and (i) population size and (ii) connectivity index. Recently-founded populations exhibited the same level of genetic diversity as ancient populations and also possessed higher plant fitness. There was no indication of strong founder effects in recently-established populations. The results suggest that the creation of habitats through human activities could provide new opportunities for conservation of this species. [source] Analyses of RAPD data for detection of host specialization in Sclerotinia homoeocarpaPLANT PATHOLOGY, Issue 2 2000T. Hsiang Upgma analysis, principal component analysis, genetic diversity analysis and genetic distance analysis of RAPD data were used to assess the extent of host specialization in 50 isolates of S. homoeocarpa from five turfgrass hosts. In upgma analysis and principal component analysis, the occurrence of host specialization was not readily apparent based on visual inspection. Genetic diversity analysis showed significant differentiation among isolates from different host species (GST = 0.34, P < 0.001). The strongest evidence for some degree of host specialization came from the statistical analysis of genetic distances among isolates. By grouping pairwise genetic distances between isolates based on their host species, and analysing for average distance within the same host species and among different host species, it was found that the average distance within species was less than among species (P < 0.0001). An analysis of molecular variance of the genetic distances among isolates found that 32.3% of the total variation was attributable to host species. It is concluded that these isolates of S. homoeocarpa showed a weak level of host specialization, which was not readily apparent by upgma or principal component analyses, but was revealed by genetic diversity analysis and statistical analysis of genetic distances among isolates. Inoculation tests on different host species and tests using a greater number of isolates are required to confirm the extent of specialization. [source] Comparison of proteomic biomarker panels in urine and serum for ovarian cancer diagnosisPROTEOMICS - CLINICAL APPLICATIONS, Issue 3 2010Anette Lykke Petri Abstract Purpose: The purposes of this study were to confirm previously found candidate epithelial ovarian cancer biomarkers in urine and to compare a paired serum biomarker panel and a urine biomarker panel from the same study cohort with regard to the receiver operating characteristic curve (ROC) area under the ROC curve (AUC) values. Experimental design: Four significant urine biomarkers were confirmed among 130 pelvic mass patients in the present study. The four biomarkers form a potential urine biomarker panel. From the same study cohort, the potential urine biomarker panel was compared to a serum biomarker panel, consisting of seven proteins/peptides, OvaRI. Results: Multivariate analysis of the urine panel demonstrated a significant differentiation (p<0.0001) between epithelial ovarian cancer patients and patients with benign ovarian pelvic masses. The ROC AUC of the urine panel was 0.84 and the ROC AUC of OvaRI was 0.83. Combining the urine panel with OvaRI demonstrated a significant contribution from both, for urine peaks, OR=2.12 and for OvaRI, OR=1.39; the ROC AUC of this model was 0.88. Conclusions and clinical relevance: We demonstrated that both urine and serum can be used individually or in combination to potentially aid in ovarian cancer diagnostics. Urine proteomic profiling could provide biomarkers for the non-invasive test required in clinical practice. [source] Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysisAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 2 2010Lars Fehren-Schmitz Abstract Alternative models have been proposed to explain the formation and decline of the south Peruvian Nasca culture, ranging from migration or invasion to autochthonous development and ecological crisis. To reveal to what extent population dynamic processes accounted for cultural development in the Nasca mainland, or were influenced by them, we analyzed ancient mitochondrial DNA of 218 individuals, originating from chronologically successive archaeological sites in the Palpa region, the Paracas Peninsula, and the Andean highlands in southern Peru. The sampling strategy allowed a diachronic analysis in a time frame from approximately 800 BC to 800 AD. Mitochondrial coding region polymorphisms were successfully analyzed and replicated for 130 individuals and control region sequences (np 16021,16408) for 104 individuals to determine Native American mitochondrial DNA haplogroups and haplotypes. The results were compared with ancient and contemporary Peruvian populations to reveal genetic relations of the archaeological samples. Frequency data and statistics show clear proximity of the Nasca populations to the populations of the preceding Paracas culture from Palpa and the Peninsula, and suggest, along with archaeological data, that the Nasca culture developed autochthonously in the Rio Grande drainage. Furthermore, the influence of changes in socioeconomic complexity in the Palpa area on the genetic diversity of the local population could be observed. In all, a strong genetic affinity between pre-Columbian coastal populations from southern Peru could be determined, together with a significant differentiation from ancient highland and all present-day Peruvian reference populations, best shown in the differential distribution of mitochondrial haplogroups. Am J Phys Anthropol 2010. © 2009 Wiley-Liss, Inc. [source] Pre-Hispanic Mesoamerican demography approximates the present-day ancestry of Mestizos throughout the territory of MexicoAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2009Rodrigo Rubi-Castellanos Abstract Over the last 500 years, admixture among Amerindians, Europeans, and Africans, principally, has come to shape the present-day gene pool of Mexicans, particularly Mestizos, who represent about 93% of the total Mexican population. In this work, we analyze the genetic data of 13 combined DNA index system-short tandem repeats (CODIS-STRs) in 1,984 unrelated Mestizos representing 10 population samples from different regions of Mexico, namely North, West, Central, and Southeast. The analysis of molecular variance (AMOVA) test demonstrated low but significant differentiation among Mestizos from different regions (FST = 0.34%; P = 0.0000). Although the spatial analysis of molecular variance (SAMOVA) predicted clustering Mestizo populations into four well-delimited groups, the main differentiation was observed between Northwest when compared with Central and Southeast regions. In addition, we included analysis of individuals of Amerindian (Purepechas), European (Huelva, Spain), and African (Fang) origin. Thus, STRUCTURE analysis was performed identifying three well-differentiated ancestral populations (k = 3). STRUCTURE results and admixture estimations by means of LEADMIX software in Mestizo populations demonstrated genetic heterogeneity or asymmetric admixture throughout Mexico, displaying an increasing North-to-South gradient of Amerindian ancestry, and vice versa regarding the European component. Interestingly, this distribution of Amerindian ancestry roughly reflects pre-Hispanic Native-population density, particularly toward the Mesoamerican area. The forensic, epidemiological, and evolutionary implications of these findings are discussed herein. Am J Phys Anthropol 2009. © 2009 Wiley-Liss, Inc. [source] Resistance and reactance in oscillation lung function reflect basal lung function and bronchial hyperresponsiveness respectivelyRESPIROLOGY, Issue 7 2009Hyeong Yoon KIM ABSTRACT Background and objective: Currently there are few data available regarding the use of impulse oscillometry parameters to assess airflow obstruction during standardized methacholine challenge testing. Methods: Methacholine challenge tests were performed using impulse oscillometry and conventional spirometry in 64 healthy and 39 asthmatic children, in order to determine airway resistance (R) and reactance (X) at frequencies of 5,35 Hz, as well as FEV1. Results: Baseline R and X were significantly different between the healthy and asthmatic children, with the most discriminating parameter being resistance at 5 Hz (R5). In asthmatic children BHR was well demonstrated by FEV1, X5 and X10, but not by R5. However, when the actual R5 values obtained in this study were compared with the predicted values, there appeared to be differences in the lung function measures that corresponded to varying methacholine concentrations. In addition, the PC20_FEV1 and PC70_X5 were significantly more sensitive than other parameters for methacholine challenge testing. Conclusions: Measuring resistance at 5 Hz using impulse oscillometry facilitates significant differentiation of baseline lung function between asthmatic and healthy children. Additionally, X may be a suitable replacement for PC20 in methacholine challenge testing. [source] Genetic diversity of captive forest musk deer (Moschus berezovskii) inferred from the mitochondrial DNA control regionANIMAL GENETICS, Issue 1 2009H. Peng Summary Forest musk deer (Moschus berezovskii) were once distributed widely in China. However, wild populations have declined dramatically because of poaching and habitat loss. Captive breeding populations have been established for several decades, but the genetic backgrounds of most captive populations were unclear and the population sizes increased very slowly. To provide useful information for conservation and management of this species, we investigated the genetic diversity and population structure of forest musk deer by analysing a 582-bp fragment of the mitochondrial DNA (mtDNA) control region (CR) in three captive breeding populations in Sichuan Province, China. Ninety-four variable sites and 27 haplotypes were observed in 109 individuals, and the nucleotide and haplotype diversities were relatively high compared with those of other endangered mammals. Of the three investigated populations, the Maerkang population had the highest nucleotide diversity (, = 0.0568), haplotype diversity (h = 0.836) and average intra-population genetic distance (0.062). The analysis of molecular variance demonstrated that most variation occurred within samples and that there was significant differentiation of the three populations. Estimates of gene flow indicated that there were few genetic exchanges among the three populations. Building pedigree records and increasing gene flow between populations will be helpful for conserving these populations and this species. [source] CYPRIOT BYZANTINE GLAZED POTTERY: A STUDY OF THE PAPHOS WORKSHOPSARCHAEOMETRY, Issue 4 2010A. C. CHARALAMBOUS Twenty-five samples of Byzantine glazed pottery from two archaeological sites between Limassol and Paphos region (Cyprus), dated between the 12th and 15th century ad were studied using micro X-ray fluorescence spectroscopy, scanning electron microscopy and X-ray diffraction analysis. It was found that all the glazes contain lead, following the main manufacturing process of medieval pottery in the Mediterranean territory, while some of them contain tin, possibly for better opacity. Furthermore, it is shown that copper, iron and cobalt with nickel are responsible for the decoration colours. Finally, the application of principal component analysis revealed significant differentiation for some of the samples. [source] Amplified fragment length polymorphism fingerprints support limited gene flow among social spider populationsBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2009DEBORAH SMITH We used DNA fingerprints to determine whether the population structure and colony composition of the cooperative social spider Stegodyphus dumicola are compatible with requirements of interdemic (,group') selection: differential proliferation of demes or groups and limited gene flow among groups. To investigate gene flow among groups, spiders were collected from nests at 21 collection sites in Namibia. Analysis of molecular variance showed a small but highly significant differentiation among geographic regions (,PT = 0.23, P = 0.001). Thirty-three nests at four collection sites (6,10 spiders per nest, 292 individual spiders) were investigated in more detail to evaluate variation within and among colonies and among collection sites. In these 33 nests, an average of 15% of loci (fingerprint bands) were polymorphic among nestmates; 16% of observed variance was partitioned among collection sites, 48% among nests within a collection site, and 36% among individuals within nests. Spatial autocorrelation analyses of spiders at three collection sites showed that the maximum extent of detectable spatial autocorrelation among individuals was approximately 30 m, indicating dispersal over greater distances is not typical. These results indicate limited gene flow among nests, as well as spatial structuring at the level of regions, local populations, and nests, compatible with interdemic selection. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 235,246. [source] | ||||||||||||||||||||||||||||||||||