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Warblers
Kinds of Warblers Terms modified by Warblers Selected AbstractsINBREEDING IN THE SEYCHELLES WARBLER: ENVIRONMENT-DEPENDENT MATERNAL EFFECTSEVOLUTION, Issue 9 2004David S. Richardson Abstract The deleterious effects of inbreeding can be substantial in wild populations and mechanisms to avoid such matings have evolved in many organisms. In situations where social mate choice is restricted, extrapair paternity may be a strategy used by females to avoid inbreeding and increase offspring heterozygosity. In the cooperatively breeding Seychelles warbler, Acrocephalus sechellensis, neither social nor extrapair mate choice was used to avoid inbreeding facultatively, and close inbreeding occurred in approximately 5% of matings. However, a higher frequency of extra-group paternity may be selected for in female subordinates because this did reduce the frequency of mating between close relatives. Inbreeding resulted in reduced individual heterozygosity, which, against expectation, had an almost significant (P= 0.052), positive effect on survival. Conversely, low heterozygosity in the genetic mother was linked to reduced offspring survival, and the magnitude of this intergenerational inbreeding depression effect was environment-dependent. Because we controlled for genetic effects and most environmental effects (through the experimental cross-fostering of nestlings), we conclude that the reduced survival was a result of maternal effects. Our results show that inbreeding can have complicated effects even within a genetic bottlenecked population where the "purging" of recessive alleles is expected to reduce the effects of inbreeding depression. [source] One Hundred Fifty Years of Change in Forest Bird Breeding Habitat: Estimates of Species DistributionsCONSERVATION BIOLOGY, Issue 6 2005LISA A. SCHULTE aptitud del hábitat; ecología aviar; ecología de paisaje; planificación de conservación Abstract:,Evaluating bird population trends requires baseline data. In North America the earliest population data available are those from the late 1960s. Forest conditions in the northern Great Lake states (U.S.A.), however, have undergone succession since the region was originally cut over around the turn of the twentieth century, and it is expected that bird populations have undergone concomitant change. We propose pre-Euro-American settlement as an alternative baseline for assessing changes in bird populations. We evaluated the amount, quality, and distribution of breeding bird habitat during the mid-1800s and early 1990s for three forest birds: the Pine Warbler (Dendroica pinus), Blackburnian Warbler (D. fusca), and Black-throated Green Warbler (D. virens). We constructed models of bird and habitat relationships based on literature review and regional data sets of bird abundance and applied these models to widely available vegetation data. Original public-land survey records represented historical habitat conditions, and a combination of forest inventory and national land-cover data represented current conditions. We assessed model robustness by comparing current habitat distribution to actual breeding bird locations from the Wisconsin Breeding Bird Atlas. The model showed little change in the overall amount of Pine Warbler habitat, whereas both the Blackburnian Warber and the Black-throated Green Warbler have experienced substantial habitat losses. For the species we examined, habitat quality has degraded since presettlement and the spatial distribution of habitat shifted among ecoregions, with range expansion accompanying forest incursion into previously open habitats or the replacement of native forests with pine plantations. Sources of habitat loss and degradation include loss of conifers and loss of large trees. Using widely available data sources in a habitat suitability model framework, our method provides a long-term analysis of change in bird habitat and a presettlement baseline for assessing current conservation priority. Resumen:,La evaluación de tendencias de las poblaciones de aves requiere de datos de referencia. En Norte América, los primeros datos disponibles de poblaciones son del final de la década de 1960. Sin embargo, las condiciones de los bosques en los estados de los Grandes Lagos (E.U.A.) han experimentado sucesión desde que la región fue talada en los inicios del siglo veinte, y se espera que las poblaciones de aves hayan experimentado cambios concomitantes. Proponemos que se considere al período previo a la colonización euro americana como referencia alternativa para evaluar los cambios en las poblaciones de aves. Evaluamos la cantidad, calidad y distribución del hábitat para reproducción de tres especies de aves de bosque (Dendroica pinus, D. fusca y D. virens) a mediados del siglo XIX e inicios del XX. Construimos modelos de las relaciones entre las aves y el hábitat con base en la literatura y conjuntos de datos de abundancia de aves y los aplicamos a los datos de vegetación ampliamente disponibles. Los registros topográficos de tierras públicas originales representaron las condiciones históricas del hábitat, y una combinación de datos del inventario forestal y de cobertura de suelo representaron las condiciones actuales. Evaluamos la robustez del modelo mediante la comparación de la distribución de hábitat actual con sitios de reproducción de aves registrados en el Wisconsin Breeding Bird Atlas. El modelo mostró poco cambio en la cantidad total de hábitat de Dendroica pinus, mientras que tanto D. fusca como D. virens han experimentado pérdidas sustanciales de hábitat. Para las especies examinadas, la calidad del hábitat se ha degradado desde antes de la colonización y la distribución espacial del hábitat cambió entre ecoregiones, con la expansión del rango acompañando la incursión de bosques en hábitats anteriormente abiertos o el reemplazo de bosques nativos con plantaciones de pinos. Las fuentes de pérdida y degradación de hábitats incluyen la pérdida de coníferas y de árboles grandes. Mediante la utilización de fuentes de datos ampliamente disponibles en un modelo de aptitud de hábitat, nuestro método proporciona un análisis a largo plazo de los cambios en el hábitat de aves y una referencia precolonización para evaluar prioridades de conservación actuales. [source] Extracting long-term patterns of population changes from sporadic counts of migrant birdsENVIRONMETRICS, Issue 5 2010Joanna Mills Flemming Abstract Declines of many North American birds are of conservation concern. For almost 40 years, experienced birders have kept daily counts of migrant landbirds during visits to Seal and Brier Islands, both of which are off Nova Scotia's southern tip. Here we assess the utility of Generalized Additive Models (GAMs) to extract patterns of population change of a common migrant to Seal Island, the Ruby-crowned Kinglet, while controlling for other influences including season, weather and effort. We also demonstrate, using counts of the Kinglet from Brier Island as well as counts of another common migrant, the Yellow-rumped Warbler, how our GAM methods can combine data from different geographic areas or distinct species. Most existing analyses of similar long-term data sets have used linear models to estimate trends. Our results and comparisons suggest that GAMs are a powerful way of extracting more information from such data. Copyright © 2009 John Wiley & Sons, Ltd. [source] Islands in a desert: breeding ecology of the African Reed Warbler Acrocephalus baeticatus in NamibiaIBIS, Issue 4 2001CORINE M. EISING The continental African Reed Warbler Acrocephalus baeticatus, like its relative the Seychelles Warbler Acrocephalus sechellensis, breeds in isolated patches. We studied the mating system of the African Reed Warbler to see whether this species, like the Seychelles Warbler, shows co-operative breeding. The African Reed Warbler is not polygynous. The majority breed monogamously (88%, n= 65), however in 12% of the territories three adult unrelated birds (mostly males) were observed participating in the brooding and feeding of nestlings, suggesting a polyandrous breeding system. Multilocus DNA fingerprinting revealed that the helping bird was unrelated to the pair birds. The percentage of nests with helpers was low compared to rates found in the Seychelles Warbler or Henderson Reed Warbler Acrocephalus vaughani taiti. This could be due to the scarcity of potential helpers or to the fact that, although limited, birds still had the opportunity to disperse within a meta-population structure in search of vacant territories. The presence of helpers was associated with increased hatching success due to lower predation rates, but not with increased fledging success. Another possible benefit of helping behaviour in this species could be improved predator detection and mobbing. Nest predation was high and warblers tended to build their nests in the highest, most dense reed patches available in their territory. There was no relation between habitat quality, measured as insect food availability, and the occurrence of helpers. [source] Continuous, age-related plumage variation in male Kirtland's WarblersJOURNAL OF FIELD ORNITHOLOGY, Issue 1 2007John R. Probst ABSTRACT The ability to age individual birds visually in the field based on plumage variation could provide important demographic and biogeographical information. We describe an approach to infer ages from a distribution of plumage scores of free-ranging male Kirtland's Warblers (Dendroica kirtlandii). We assigned ages to males using a scoring scheme (0,12 points) based on variation in plumage coloration, brightness, and contrast on three dorsal and three ventral body regions presumed to be age-related. The distribution of total additive plumage scores for 875 breeding males was normally distributed, indicating no distinct age classes. Thus, we developed provisional plumage-age classes of second year (SY) and after second-year (ASY), and compared them to the total plumage scores of a smaller subsample of known age (N= 92) and minimum age (N= 143) males. Plumage scores of known-age male Kirtland's Warblers increased nonlinearly with age (rs= 0.67), but with some overlap. The median plumage score for SY males (median = 5.0) was significantly lower than for third-year (TY) males (median = 7.0) and after third-year (3 year and older) males (median = 8.0), indicating that the plumage of male Kirtland's Warblers becomes more distinctive and brighter with age. Linear discriminant function analysis differentiated ASY male Kirtland's Warbler from SY males with 78.3% accuracy. Investigators could use the distribution of plumage scores and approximate age structures to document changes in male age structure during colonization, use, and abandonment of habitats by Kirtland's Warblers or other species that occupy early successional habitats. Aging free-ranging birds based on a plumage scoring scheme may be especially critical for demographic studies of less-studied species where it is unlikely that a banding program will be initiated, but where plumage-age inferences or management decisions must be made. SINOPSIS Describimos una forma para inferir la edad a través de una distribución de marcadores en machos silvestres de la reinita Dendroica kirtlandii. Utilizando dicho acercamiento, asignamos edad relativa a machos basándonos en un esquema de puntuación (0,12) para la coloración del plumaje, su brillantez, y contraste en tres localidades del dorso y la parte ventral, que han sido relacionadas con la edad de estos. La distribución de las puntuaciones de 875 machos fue normal, lo que indica que no hubo forma de distinguir las diferentes edades. Por ende, desarrollamos un divisiones de clases, basándonos en diferencias en el plumaje para individuos de segundo año (SA) y posterior al segundo año (PSA) y los comparamos a las puntuaciones de una pequeña muestra de aves (N= 92) cuya edad era conocida y a otra en que sabíamos la edad mínima (N= 143). La puntuación total para individuos de edad conocida aumento de forma no-lineal con la edad (Rs = 0.67), con un pequeño solapamiento en el plumaje total. La puntuación para machos de segundo año (SA) (mediana = 5.0) fue significativamente menor que para aves de tercer año (mediana = 7.0) y esta a su vez que para aves mayores a tres años (mediana = 8.0), lo que indica que el plumaje de los machos, en las aves estudiadas, se torna más brillante con la edad. Un análisis lineal de función discriminativa pudo diferenciar entre aves PSA y SA con un 78.3% de exactitud. Los investigadores han utilizado estas diferencias en el plumaje para clasificar entre los grupos machos territoriales que no han sido anillados. También pudieran utilizar estas particularidades y diferencias en el plumaje para aproximar la estructura de edades entre machos silvestres y hacer inferencias sobre la demografía y reclutamiento de aves en habitats de diferente calidad. [source] Temporal fluctuation in abundance of Brown-headed Cowbirds and their hosts in riparian habitat in the Okanagan Valley, British Columbia, CanadaJOURNAL OF FIELD ORNITHOLOGY, Issue 4 2006Tawna C. Morgan ABSTRACT We tested the hypothesis that the abundance of Brown-headed Cowbirds (Molothrus ater) and their hosts, as well as parasitism rates, changed between 1992,1993 and 2001,2003 in riparian habitats in the Okanagan Valley, British Columbia, Canada, where riparian habitat has been reduced in area by more than 85% over the past 60 years. Cowbird abundance declined from a mean of 2.1 and 1.9 individuals per census plot in 1992 and 1993, respectively, to 0.66 individuals per plot in 2001,2002. The mean number of potential host individuals per census plot was also lower in 2001,2002 (5.5) than in 1992 (7.0) and 1993 (7.8). Although the percentage of Yellow Warbler (Dendroica petechia) nests parasitized declined (77% in 1992,1993 to 50% in 2002,2003), Yellow Warblers and Song Sparrows (Melospiza melodia) in the Okanagan Valley continue to be parasitized at high rates and have low nesting success. Host species and the distance of nests from the edge of nest patches were the strongest predictors of both nest success and parasitism, indicating the importance of large continuous patches of shrubs that allow nests to be located further from edges. SINOPSIS Se expuso a pruebas la hipótesis de la abundancia de tordos (Molothrus ater) y sus huespedes y como la tasa de parasitismo cambiaron durante el 1992,1993 y el 2001,2002 en un hábitat ripario en el valle Okanagan, Columbia Británica, Canada. En dicha localidad el hábitat ripario se redujo en un 85% en los últimos 60 años. La abundancia de tordos se redujo en un promedio de 2.1 y 1.9 de individuos/censo en 1992 y 1992, respectivamente, a 0.66 individuos en 2001,2002. El número promedio de hospederos potenciales por localidad censada (5.5) fue menor para el mismo periodo en comparación con el 1992 (7.0) y el 1993 (7.8). Aunque el porcentaje de nidos parasitados (77% en el 1992,1993 a 50% en 2002,2003) en Dendroica petechia, se redujo, tanto la especie como Melospiza melodia, tuvieron un alto grado de parasitismo y un bajo éxito de anidamiento. Tanto las especies hospederas y la distancia del nido al borde del parcho de anidamiento resultaron ser los elementos de predicción más fuertes con respecto al parasitismo y el éxito de anidamiento. Esto es un indicativo claro de la importancia de parchos de arbustos amplios y contínuos, que permitan el anidamiento lejos del borde. [source] Short-Term Response of Land Birds to Ponderosa Pine RestorationRESTORATION ECOLOGY, Issue 4 2007William L. Gaines Abstract We monitored the short-term (>3 years) response of land birds to forest restoration treatments in Ponderosa pine forests located on the east slope of the North Cascade Range. Restoration treatments were designed to create stand structure and composition similar to pre-settlement forests, which were influenced by a frequent fire regime. Overall, avian community composition was changed as a result of the treatments. Cassin's Finch, Chipping Sparrow, and Yellow-rumped Warbler were found at higher densities in treated stands, whereas Mountain Chickadee, Western Tanager, and Red-breasted Nuthatch had higher densities in untreated stands. White-headed Woodpecker and Western Bluebird were only detected in the treated stands. Brown-headed Cowbird showed no response to treatments. We detected changes in the density of four of five foraging guilds in response to restoration treatments. Tree seedeaters, low understory and ground insectivores, and aerial insectivores all increased in density in treated stands. Overall, bark insectivores showed no density response to treatments. Tree foliage insectivore density was lower in treated than in untreated stands. Overall avian density, density of neotropical migrants, and density of some focal species were higher in treated stands. Monitoring should be continued to understand the longer-term (5,10 year) responses of land birds and to guide future forest restoration efforts. [source] European Mathematical Genetics Meeting, Heidelberg, Germany, 12th,13th April 2007ANNALS OF HUMAN GENETICS, Issue 4 2007Article first published online: 28 MAY 200 Saurabh Ghosh 11 Indian Statistical Institute, Kolkata, India High correlations between two quantitative traits may be either due to common genetic factors or common environmental factors or a combination of both. In this study, we develop statistical methods to extract the contribution of a common QTL to the total correlation between the components of a bivariate phenotype. Using data on bivariate phenotypes and marker genotypes for sib-pairs, we propose a test for linkage between a common QTL and a marker locus based on the conditional cross-sib trait correlations (trait 1 of sib 1 , trait 2 of sib 2 and conversely) given the identity-by-descent sharing at the marker locus. The null hypothesis cannot be rejected unless there exists a common QTL. We use Monte-Carlo simulations to evaluate the performance of the proposed test under different trait parameters and quantitative trait distributions. An application of the method is illustrated using data on two alcohol-related phenotypes from the Collaborative Study On The Genetics Of Alcoholism project. Rémi Kazma 1 , Catherine Bonaïti-Pellié 1 , Emmanuelle Génin 12 INSERM UMR-S535 and Université Paris Sud, Villejuif, 94817, France Keywords: Gene-environment interaction, sibling recurrence risk, exposure correlation Gene-environment interactions may play important roles in complex disease susceptibility but their detection is often difficult. Here we show how gene-environment interactions can be detected by investigating the degree of familial aggregation according to the exposure of the probands. In case of gene-environment interaction, the distribution of genotypes of affected individuals, and consequently the risk in relatives, depends on their exposure. We developed a test comparing the risks in sibs according to the proband exposure. To evaluate the properties of this new test, we derived the formulas for calculating the expected risks in sibs according to the exposure of probands for various values of exposure frequency, relative risk due to exposure alone, frequencies of latent susceptibility genotypes, genetic relative risks and interaction coefficients. We find that the ratio of risks when the proband is exposed and not exposed is a good indicator of the interaction effect. We evaluate the power of the test for various sample sizes of affected individuals. We conclude that this test is valuable for diseases with moderate familial aggregation, only when the role of the exposure has been clearly evidenced. Since a correlation for exposure among sibs might lead to a difference in risks among sibs in the different proband exposure strata, we also add an exposure correlation coefficient in the model. Interestingly, we find that when this correlation is correctly accounted for, the power of the test is not decreased and might even be significantly increased. Andrea Callegaro 1 , Hans J.C. Van Houwelingen 1 , Jeanine Houwing-Duistermaat 13 Dept. of Medical Statistics and Bioinformatics, Leiden University Medical Center, The Netherlands Keywords: Survival analysis, age at onset, score test, linkage analysis Non parametric linkage (NPL) analysis compares the identical by descent (IBD) sharing in sibling pairs to the expected IBD sharing under the hypothesis of no linkage. Often information is available on the marginal cumulative hazards (for example breast cancer incidence curves). Our aim is to extend the NPL methods by taking into account the age at onset of selected sibling pairs using these known marginal hazards. Li and Zhong (2002) proposed a (retrospective) likelihood ratio test based on an additive frailty model for genetic linkage analysis. From their model we derive a score statistic for selected samples which turns out to be a weighed NPL method. The weights depend on the marginal cumulative hazards and on the frailty parameter. A second approach is based on a simple gamma shared frailty model. Here, we simply test whether the score function of the frailty parameter depends on the excess IBD. We compare the performance of these methods using simulated data. Céline Bellenguez 1 , Carole Ober 2 , Catherine Bourgain 14 INSERM U535 and University Paris Sud, Villejuif, France 5 Department of Human Genetics, The University of Chicago, USA Keywords: Linkage analysis, linkage disequilibrium, high density SNP data Compared with microsatellite markers, high density SNP maps should be more informative for linkage analyses. However, because they are much closer, SNPs present important linkage disequilibrium (LD), which biases classical nonparametric multipoint analyses. This problem is even stronger in population isolates where LD extends over larger regions with a more stochastic pattern. We investigate the issue of linkage analysis with a 500K SNP map in a large and inbred 1840-member Hutterite pedigree, phenotyped for asthma. Using an efficient pedigree breaking strategy, we first identified linked regions with a 5cM microsatellite map, on which we focused to evaluate the SNP map. The only method that models LD in the NPL analysis is limited in both the pedigree size and the number of markers (Abecasis and Wigginton, 2005) and therefore could not be used. Instead, we studied methods that identify sets of SNPs with maximum linkage information content in our pedigree and no LD-driven bias. Both algorithms that directly remove pairs of SNPs in high LD and clustering methods were evaluated. Null simulations were performed to control that Zlr calculated with the SNP sets were not falsely inflated. Preliminary results suggest that although LD is strong in such populations, linkage information content slightly better than that of microsatellite maps can be extracted from dense SNP maps, provided that a careful marker selection is conducted. In particular, we show that the specific LD pattern requires considering LD between a wide range of marker pairs rather than only in predefined blocks. Peter Van Loo 1,2,3 , Stein Aerts 1,2 , Diether Lambrechts 4,5 , Bernard Thienpont 2 , Sunit Maity 4,5 , Bert Coessens 3 , Frederik De Smet 4,5 , Leon-Charles Tranchevent 3 , Bart De Moor 2 , Koen Devriendt 3 , Peter Marynen 1,2 , Bassem Hassan 1,2 , Peter Carmeliet 4,5 , Yves Moreau 36 Department of Molecular and Developmental Genetics, VIB, Belgium 7 Department of Human Genetics, University of Leuven, Belgium 8 Bioinformatics group, Department of Electrical Engineering, University of Leuven, Belgium 9 Department of Transgene Technology and Gene Therapy, VIB, Belgium 10 Center for Transgene Technology and Gene Therapy, University of Leuven, Belgium Keywords: Bioinformatics, gene prioritization, data fusion The identification of genes involved in health and disease remains a formidable challenge. Here, we describe a novel bioinformatics method to prioritize candidate genes underlying pathways or diseases, based on their similarity to genes known to be involved in these processes. It is freely accessible as an interactive software tool, ENDEAVOUR, at http://www.esat.kuleuven.be/endeavour. Unlike previous methods, ENDEAVOUR generates distinct prioritizations from multiple heterogeneous data sources, which are then integrated, or fused, into one global ranking using order statistics. ENDEAVOUR prioritizes candidate genes in a three-step process. First, information about a disease or pathway is gathered from a set of known "training" genes by consulting multiple data sources. Next, the candidate genes are ranked based on similarity with the training properties obtained in the first step, resulting in one prioritized list for each data source. Finally, ENDEAVOUR fuses each of these rankings into a single global ranking, providing an overall prioritization of the candidate genes. Validation of ENDEAVOUR revealed it was able to efficiently prioritize 627 genes in disease data sets and 76 genes in biological pathway sets, identify candidates of 16 mono- or polygenic diseases, and discover regulatory genes of myeloid differentiation. Furthermore, the approach identified YPEL1 as a novel gene involved in craniofacial development from a 2-Mb chromosomal region, deleted in some patients with DiGeorge-like birth defects. Finally, we are currently evaluating a pipeline combining array-CGH, ENDEAVOUR and in vivo validation in zebrafish to identify novel genes involved in congenital heart defects. Mark Broom 1 , Graeme Ruxton 2 , Rebecca Kilner 311 Mathematics Dept., University of Sussex, UK 12 Division of Environmental and Evolutionary Biology, University of Glasgow, UK 13 Department of Zoology, University of Cambridge, UK Keywords: Evolutionarily stable strategy, parasitism, asymmetric game Brood parasites chicks vary in the harm that they do to their companions in the nest. In this presentation we use game-theoretic methods to model this variation. Our model considers hosts which potentially abandon single nestlings and instead choose to re-allocate their reproductive effort to future breeding, irrespective of whether the abandoned chick is the host's young or a brood parasite's. The parasite chick must decide whether or not to kill host young by balancing the benefits from reduced competition in the nest against the risk of desertion by host parents. The model predicts that three different types of evolutionarily stable strategies can exist. (1) Hosts routinely rear depleted broods, the brood parasite always kills host young and the host never then abandons the nest. (2) When adult survival after deserting single offspring is very high, hosts always abandon broods of a single nestling and the parasite never kills host offspring, effectively holding them as hostages to prevent nest desertion. (3) Intermediate strategies, in which parasites sometimes kill their nest-mates and host parents sometimes desert nests that contain only a single chick, can also be evolutionarily stable. We provide quantitative descriptions of how the values given to ecological and behavioral parameters of the host-parasite system influence the likelihood of each strategy and compare our results with real host-brood parasite associations in nature. Martin Harrison 114 Mathematics Dept, University of Sussex, UK Keywords: Brood parasitism, games, host, parasite The interaction between hosts and parasites in bird populations has been studied extensively. Game theoretical methods have been used to model this interaction previously, but this has not been studied extensively taking into account the sequential nature of this game. We consider a model allowing the host and parasite to make a number of decisions, which depend on a number of natural factors. The host lays an egg, a parasite bird will arrive at the nest with a certain probability and then chooses to destroy a number of the host eggs and lay one of it's own. With some destruction occurring, either natural or through the actions of the parasite, the host chooses to continue, eject an egg (hoping to eject the parasite) or abandon the nest. Once the eggs have hatched the game then falls to the parasite chick versus the host. The chick chooses to destroy or eject a number of eggs. The final decision is made by the host, choosing whether to raise or abandon the chicks that are in the nest. We consider various natural parameters and probabilities which influence these decisions. We then use this model to look at real-world situations of the interactions of the Reed Warbler and two different parasites, the Common Cuckoo and the Brown-Headed Cowbird. These two parasites have different methods in the way that they parasitize the nests of their hosts. The hosts in turn have a different reaction to these parasites. Arne Jochens 1 , Amke Caliebe 2 , Uwe Roesler 1 , Michael Krawczak 215 Mathematical Seminar, University of Kiel, Germany 16 Institute of Medical Informatics and Statistics, University of Kiel, Germany Keywords: Stepwise mutation model, microsatellite, recursion equation, temporal behaviour We consider the stepwise mutation model which occurs, e.g., in microsatellite loci. Let X(t,i) denote the allelic state of individual i at time t. We compute expectation, variance and covariance of X(t,i), i=1,,,N, and provide a recursion equation for P(X(t,i)=z). Because the variance of X(t,i) goes to infinity as t grows, for the description of the temporal behaviour, we regard the scaled process X(t,i)-X(t,1). The results furnish a better understanding of the behaviour of the stepwise mutation model and may in future be used to derive tests for neutrality under this model. Paul O'Reilly 1 , Ewan Birney 2 , David Balding 117 Statistical Genetics, Department of Epidemiology and Public Health, Imperial, College London, UK 18 European Bioinformatics Institute, EMBL, Cambridge, UK Keywords: Positive selection, Recombination rate, LD, Genome-wide, Natural Selection In recent years efforts to develop population genetics methods that estimate rates of recombination and levels of natural selection in the human genome have intensified. However, since the two processes have an intimately related impact on genetic variation their inference is vulnerable to confounding. Genomic regions subject to recent selection are likely to have a relatively recent common ancestor and consequently less opportunity for historical recombinations that are detectable in contemporary populations. Here we show that selection can reduce the population-based recombination rate estimate substantially. In genome-wide studies for detecting selection we observe a tendency to highlight loci that are subject to low levels of recombination. We find that the outlier approach commonly adopted in such studies may have low power unless variable recombination is accounted for. We introduce a new genome-wide method for detecting selection that exploits the sensitivity to recent selection of methods for estimating recombination rates, while accounting for variable recombination using pedigree data. Through simulations we demonstrate the high power of the Ped/Pop approach to discriminate between neutral and adaptive evolution, particularly in the context of choosing outliers from a genome-wide distribution. Although methods have been developed showing good power to detect selection ,in action', the corresponding window of opportunity is small. In contrast, the power of the Ped/Pop method is maintained for many generations after the fixation of an advantageous variant Sarah Griffiths 1 , Frank Dudbridge 120 MRC Biostatistics Unit, Cambridge, UK Keywords: Genetic association, multimarker tag, haplotype, likelihood analysis In association studies it is generally too expensive to genotype all variants in all subjects. We can exploit linkage disequilibrium between SNPs to select a subset that captures the variation in a training data set obtained either through direct resequencing or a public resource such as the HapMap. These ,tag SNPs' are then genotyped in the whole sample. Multimarker tagging is a more aggressive adaptation of pairwise tagging that allows for combinations of two or more tag SNPs to predict an untyped SNP. Here we describe a new method for directly testing the association of an untyped SNP using a multimarker tag. Previously, other investigators have suggested testing a specific tag haplotype, or performing a weighted analysis using weights derived from the training data. However these approaches do not properly account for the imperfect correlation between the tag haplotype and the untyped SNP. Here we describe a straightforward approach to testing untyped SNPs using a missing-data likelihood analysis, including the tag markers as nuisance parameters. The training data is stacked on top of the main body of genotype data so there is information on how the tag markers predict the genotype of the untyped SNP. The uncertainty in this prediction is automatically taken into account in the likelihood analysis. This approach yields more power and also a more accurate prediction of the odds ratio of the untyped SNP. Anke Schulz 1 , Christine Fischer 2 , Jenny Chang-Claude 1 , Lars Beckmann 121 Division of Cancer Epidemiology, German Cancer Research Center (DKFZ) Heidelberg, Germany 22 Institute of Human Genetics, University of Heidelberg, Germany Keywords: Haplotype, haplotype sharing, entropy, Mantel statistics, marker selection We previously introduced a new method to map genes involved in complex diseases, using haplotype sharing-based Mantel statistics to correlate genetic and phenotypic similarity. Although the Mantel statistic is powerful in narrowing down candidate regions, the precise localization of a gene is hampered in genomic regions where linkage disequilibrium is so high that neighboring markers are found to be significant at similar magnitude and we are not able to discriminate between them. Here, we present a new approach to localize susceptibility genes by combining haplotype sharing-based Mantel statistics with an iterative entropy-based marker selection algorithm. For each marker at which the Mantel statistic is evaluated, the algorithm selects a subset of surrounding markers. The subset is chosen to maximize multilocus linkage disequilibrium, which is measured by the normalized entropy difference introduced by Nothnagel et al. (2002). We evaluated the algorithm with respect to type I error and power. Its ability to localize the disease variant was compared to the localization (i) without marker selection and (ii) considering haplotype block structure. Case-control samples were simulated from a set of 18 haplotypes, consisting of 15 SNPs in two haplotype blocks. The new algorithm gave correct type I error and yielded similar power to detect the disease locus compared to the alternative approaches. The neighboring markers were clearly less often significant than the causal locus, and also less often significant compared to the alternative approaches. Thus the new algorithm improved the precision of the localization of susceptibility genes. Mark M. Iles 123 Section of Epidemiology and Biostatistics, LIMM, University of Leeds, UK Keywords: tSNP, tagging, association, HapMap Tagging SNPs (tSNPs) are commonly used to capture genetic diversity cost-effectively. However, it is important that the efficacy of tSNPs is correctly estimated, otherwise coverage may be insufficient. If the pilot sample from which tSNPs are chosen is too small or the initial marker map too sparse, tSNP efficacy may be overestimated. An existing estimation method based on bootstrapping goes some way to correct for insufficient sample size and overfitting, but does not completely solve the problem. We describe a novel method, based on exclusion of haplotypes, that improves on the bootstrap approach. Using simulated data, the extent of the sample size problem is investigated and the performance of the bootstrap and the novel method are compared. We incorporate an existing method adjusting for marker density by ,SNP-dropping'. We find that insufficient sample size can cause large overestimates in tSNP efficacy, even with as many as 100 individuals, and the problem worsens as the region studied increases in size. Both the bootstrap and novel method correct much of this overestimate, with our novel method consistently outperforming the bootstrap method. We conclude that a combination of insufficient sample size and overfitting may lead to overestimation of tSNP efficacy and underpowering of studies based on tSNPs. Our novel approach corrects for much of this bias and is superior to the previous method. Sample sizes larger than previously suggested may still be required for accurate estimation of tSNP efficacy. This has obvious ramifications for the selection of tSNPs from HapMap data. Claudio Verzilli 1 , Juliet Chapman 1 , Aroon Hingorani 2 , Juan Pablo-Casas 1 , Tina Shah 2 , Liam Smeeth 1 , John Whittaker 124 Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, UK 25 Division of Medicine, University College London, UK Keywords: Meta-analysis, Genetic association studies We present a Bayesian hierarchical model for the meta-analysis of candidate gene studies with a continuous outcome. Such studies often report results from association tests for different, possibly study-specific and non-overlapping markers (typically SNPs) in the same genetic region. Meta analyses of the results at each marker in isolation are seldom appropriate as they ignore the correlation that may exist between markers due to linkage disequlibrium (LD) and cannot assess the relative importance of variants at each marker. Also such marker-wise meta analyses are restricted to only those studies that have typed the marker in question, with a potential loss of power. A better strategy is one which incorporates information about the LD between markers so that any combined estimate of the effect of each variant is corrected for the effect of other variants, as in multiple regression. Here we develop a Bayesian hierarchical linear regression that models the observed genotype group means and uses pairwise LD measurements between markers as prior information to make posterior inference on adjusted effects. The approach is applied to the meta analysis of 24 studies assessing the effect of 7 variants in the C-reactive protein (CRP) gene region on plasma CRP levels, an inflammatory biomarker shown in observational studies to be positively associated with cardiovascular disease. Cathryn M. Lewis 1 , Christopher G. Mathew 1 , Theresa M. Marteau 226 Dept. of Medical and Molecular Genetics, King's College London, UK 27 Department of Psychology, King's College London, UK Keywords: Risk, genetics, CARD15, smoking, model Recently progress has been made in identifying mutations that confer susceptibility to complex diseases, with the potential to use these mutations in determining disease risk. We developed methods to estimate disease risk based on genotype relative risks (for a gene G), exposure to an environmental factor (E), and family history (with recurrence risk ,R for a relative of type R). ,R must be partitioned into the risk due to G (which is modelled independently) and the residual risk. The risk model was then applied to Crohn's disease (CD), a severe gastrointestinal disease for which smoking increases disease risk approximately 2-fold, and mutations in CARD15 confer increased risks of 2.25 (for carriers of a single mutation) and 9.3 (for carriers of two mutations). CARD15 accounts for only a small proportion of the genetic component of CD, with a gene-specific ,S, CARD15 of 1.16, from a total sibling relative risk of ,S= 27. CD risks were estimated for high-risk individuals who are siblings of a CD case, and who also smoke. The CD risk to such individuals who carry two CARD15 mutations is approximately 0.34, and for those carrying a single CARD15 mutation the risk is 0.08, compared to a population prevalence of approximately 0.001. These results imply that complex disease genes may be valuable in estimating with greater precision than has hitherto been possible disease risks in specific, easily identified subgroups of the population with a view to prevention. Yurii Aulchenko 128 Department of Epidemiology & Biostatistics, Erasmus Medical Centre Rotterdam, The Netherlands Keywords: Compression, information, bzip2, genome-wide SNP data, statistical genetics With advances in molecular technology, studies accessing millions of genetic polymorphisms in thousands of study subjects will soon become common. Such studies generate large amounts of data, whose effective storage and management is a challenge to the modern statistical genetics. Standard file compression utilities, such as Zip, Gzip and Bzip2, may be helpful to minimise the storage requirements. Less obvious is the fact that the data compression techniques may be also used in the analysis of genetic data. It is known that the efficiency of a particular compression algorithm depends on the probability structure of the data. In this work, we compared different standard and customised tools using the data from human HapMap project. Secondly, we investigate the potential uses of data compression techniques for the analysis of linkage, association and linkage disequilibrium Suzanne Leal 1 , Bingshan Li 129 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA Keywords: Consanguineous pedigrees, missing genotype data Missing genotype data can increase false-positive evidence for linkage when either parametric or nonparametric analysis is carried out ignoring intermarker linkage disequilibrium (LD). Previously it was demonstrated by Huang et al (2005) that no bias occurs in this situation for affected sib-pairs with unrelated parents when either both parents are genotyped or genotype data is available for two additional unaffected siblings when parental genotypes are missing. However, this is not the case for consanguineous pedigrees, where missing genotype data for any pedigree member within a consanguinity loop can increase false-positive evidence of linkage. The false-positive evidence for linkage is further increased when cryptic consanguinity is present. The amount of false-positive evidence for linkage is highly dependent on which family members are genotyped. When parental genotype data is available, the false-positive evidence for linkage is usually not as strong as when parental genotype data is unavailable. Which family members will aid in the reduction of false-positive evidence of linkage is highly dependent on which other family members are genotyped. For a pedigree with an affected proband whose first-cousin parents have been genotyped, further reduction in the false-positive evidence of linkage can be obtained by including genotype data from additional affected siblings of the proband or genotype data from the proband's sibling-grandparents. When parental genotypes are not available, false-positive evidence for linkage can be reduced by including in the analysis genotype data from either unaffected siblings of the proband or the proband's married-in-grandparents. Najaf Amin 1 , Yurii Aulchenko 130 Department of Epidemiology & Biostatistics, Erasmus Medical Centre Rotterdam, The Netherlands Keywords: Genomic Control, pedigree structure, quantitative traits The Genomic Control (GC) method was originally developed to control for population stratification and cryptic relatedness in association studies. This method assumes that the effect of population substructure on the test statistics is essentially constant across the genome, and therefore unassociated markers can be used to estimate the effect of confounding onto the test statistic. The properties of GC method were extensively investigated for different stratification scenarios, and compared to alternative methods, such as the transmission-disequilibrium test. The potential of this method to correct not for occasional cryptic relations, but for regular pedigree structure, however, was not investigated before. In this work we investigate the potential of the GC method for pedigree-based association analysis of quantitative traits. The power and type one error of the method was compared to standard methods, such as the measured genotype (MG) approach and quantitative trait transmission-disequilibrium test. In human pedigrees, with trait heritability varying from 30 to 80%, the power of MG and GC approach was always higher than that of TDT. GC had correct type 1 error and its power was close to that of MG under moderate heritability (30%), but decreased with higher heritability. William Astle 1 , Chris Holmes 2 , David Balding 131 Department of Epidemiology and Public Health, Imperial College London, UK 32 Department of Statistics, University of Oxford, UK Keywords: Population structure, association studies, genetic epidemiology, statistical genetics In the analysis of population association studies, Genomic Control (Devlin & Roeder, 1999) (GC) adjusts the Armitage test statistic to correct the type I error for the effects of population substructure, but its power is often sub-optimal. Turbo Genomic Control (TGC) generalises GC to incorporate co-variation of relatedness and phenotype, retaining control over type I error while improving power. TGC is similar to the method of Yu et al. (2006), but we extend it to binary (case-control) in addition to quantitative phenotypes, we implement improved estimation of relatedness coefficients, and we derive an explicit statistic that generalizes the Armitage test statistic and is fast to compute. TGC also has similarities to EIGENSTRAT (Price et al., 2006) which is a new method based on principle components analysis. The problems of population structure(Clayton et al., 2005) and cryptic relatedness (Voight & Pritchard, 2005) are essentially the same: if patterns of shared ancestry differ between cases and controls, whether distant (coancestry) or recent (cryptic relatedness), false positives can arise and power can be diminished. With large numbers of widely-spaced genetic markers, coancestry can now be measured accurately for each pair of individuals via patterns of allele-sharing. Instead of modelling subpopulations, we work instead with a coancestry coefficient for each pair of individuals in the study. We explain the relationships between TGC, GC and EIGENSTRAT. We present simulation studies and real data analyses to illustrate the power advantage of TGC in a range of scenarios incorporating both substructure and cryptic relatedness. References Clayton, D. G.et al. (2005) Population structure, differential bias and genomic control in a large-scale case-control association study. Nature Genetics37(11) November 2005. Devlin, B. & Roeder, K. (1999) Genomic control for association studies. Biometics55(4) December 1999. Price, A. L.et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics38(8) (August 2006). Voight, B. J. & Pritchard, J. K. (2005) Confounding from cryptic relatedness in case-control association studies. Public Library of Science Genetics1(3) September 2005. Yu, J.et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics38(2) February 2006. Hervé Perdry 1 , Marie-Claude Babron 1 , Françoise Clerget-Darpoux 133 INSERM U535 and Univ. Paris Sud, UMR-S 535, Villejuif, France Keywords: Modifier genes, case-parents trios, ordered transmission disequilibrium test A modifying locus is a polymorphic locus, distinct from the disease locus, which leads to differences in the disease phenotype, either by modifying the penetrance of the disease allele, or by modifying the expression of the disease. The effect of such a locus is a clinical heterogeneity that can be reflected by the values of an appropriate covariate, such as the age of onset, or the severity of the disease. We designed the Ordered Transmission Disequilibrium Test (OTDT) to test for a relation between the clinical heterogeneity, expressed by the covariate, and marker genotypes of a candidate gene. The method applies to trio families with one affected child and his parents. Each family member is genotyped at a bi-allelic marker M of a candidate gene. To each of the families is associated a covariate value; the families are ordered on the values of this covariate. As the TDT (Spielman et al. 1993), the OTDT is based on the observation of the transmission rate T of a given allele at M. The OTDT aims to find a critical value of the covariate which separates the sample of families in two subsamples in which the transmission rates are significantly different. We investigate the power of the method by simulations under various genetic models and covariate distributions. Acknowledgments H Perdry is funded by ARSEP. Pascal Croiseau 1 , Heather Cordell 2 , Emmanuelle Génin 134 INSERM U535 and University Paris Sud, UMR-S535, Villejuif, France 35 Institute of Human Genetics, Newcastle University, UK Keywords: Association, missing data, conditionnal logistic regression Missing data is an important problem in association studies. Several methods used to test for association need that individuals be genotyped at the full set of markers. Individuals with missing data need to be excluded from the analysis. This could involve an important decrease in sample size and a loss of information. If the disease susceptibility locus (DSL) is poorly typed, it is also possible that a marker in linkage disequilibrium gives a stronger association signal than the DSL. One may then falsely conclude that the marker is more likely to be the DSL. We recently developed a Multiple Imputation method to infer missing data on case-parent trios Starting from the observed data, a few number of complete data sets are generated by Markov-Chain Monte Carlo approach. These complete datasets are analysed using standard statistical package and the results are combined as described in Little & Rubin (2002). Here we report the results of simulations performed to examine, for different patterns of missing data, how often the true DSL gives the highest association score among different loci in LD. We found that multiple imputation usually correctly detect the DSL site even if the percentage of missing data is high. This is not the case for the naïve approach that consists in discarding trios with missing data. In conclusion, Multiple imputation presents the advantage of being easy to use and flexible and is therefore a promising tool in the search for DSL involved in complex diseases. Salma Kotti 1 , Heike Bickeböller 2 , Françoise Clerget-Darpoux 136 University Paris Sud, UMR-S535, Villejuif, France 37 Department of Genetic Epidemiology, Medical School, University of Göttingen, Germany Keywords: Genotype relative risk, internal controls, Family based analyses Family based analyses using internal controls are very popular both for detecting the effect of a genetic factor and for estimating the relative disease risk on the corresponding genotypes. Two different procedures are often applied to reconstitute internal controls. The first one considers one pseudocontrol genotype formed by the parental non-transmitted alleles called also 1:1 matching of alleles, while the second corresponds to three pseudocontrols corresponding to all genotypes formed by the parental alleles except the one of the case (1:3 matching). Many studies have compared between the two procedures in terms of the power and have concluded that the difference depends on the underlying genetic model and the allele frequencies. However, the estimation of the Genotype Relative Risk (GRR) under the two procedures has not been studied. Based on the fact that on the 1:1 matching, the control group is composed of the alleles untransmitted to the affected child and on the 1:3 matching, the control group is composed amongst alleles already transmitted to the affected child, we expect a difference on the GRR estimation. In fact, we suspect that the second procedure leads to biased estimation of the GRRs. We will analytically derive the GRR estimators for the 1:1 and 1:3 matching and will present the results at the meeting. Family based analyses using internal controls are very popular both for detecting the effect of a genetic factor and for estimating the relative disease risk on the corresponding genotypes. Two different procedures are often applied to reconstitute internal controls. The first one considers one pseudocontrol genotype formed by the parental non-transmitted alleles called also 1:1 matching of alleles, while the second corresponds to three pseudocontrols corresponding to all genotypes formed by the parental alleles except the one of the case (1:3 matching). Many studies have compared between the two procedures in terms of the power and have concluded that the difference depends on the underlying genetic model and the allele frequencies. However, the estimation of the Genotype Relative Risk (GRR) under the two procedures has not been studied. Based on the fact that on the 1:1 matching, the control group is composed of the alleles untransmitted to the affected child and on the 1:3 matching, the control group is composed amongst alleles already transmitted to the affected child, we expect a difference on the GRR estimation. In fact, we suspect that the second procedure leads to biased estimation of the GRR. We will analytically derive the GRR estimator for the 1:1 and 1:3 matching and will present the results at the meeting. Luigi Palla 1 , David Siegmund 239 Department of Mathematics,Free University Amsterdam, The Netherlands 40 Department of Statistics, Stanford University, California, USA Keywords: TDT, assortative mating, inbreeding, statistical power A substantial amount of Assortative Mating (AM) is often recorded on physical and psychological, dichotomous as well as quantitative traits that are supposed to have a multifactorial genetic component. In particular AM has the effect of increasing the genetic variance, even more than inbreeding because it acts across loci beside within loci, when the trait has a multifactorial origin. Under the assumption of a polygenic model for AM dating back to Wright (1921) and refined by Crow and Felsenstein (1968,1982), the effect of assortative mating on the power to detect genetic association in the Transmission Disequilibrium Test (TDT) is explored as parameters, such as the effective number of genes and the allelic frequency vary. The power is reflected by the non centrality parameter of the TDT and is expressed as a function of the number of trios, the relative risk of the heterozygous genotype and the allele frequency (Siegmund and Yakir, 2007). The noncentrality parameter of the relevant score statistic is updated considering the effect of AM which is expressed in terms of an ,effective' inbreeding coefficient. In particular, for dichotomous traits it is apparent that the higher the number of genes involved in the trait, the lower the loss in power due to AM. Finally an attempt is made to extend this relation to the Q-TDT (Rabinowitz, 1997), which involves considering the effect of AM also on the phenotypic variance of the trait of interest, under the assumption that AM affects only its additive genetic component. References Crow, & Felsenstein, (1968). The effect of assortative mating on the genetic composition of a population. Eugen.Quart.15, 87,97. Rabinowitz,, 1997. A Transmission Disequilibrium Test for Quantitative Trait Loci. Human Heredity47, 342,350. Siegmund, & Yakir, (2007) Statistics of gene mapping, Springer. Wright, (1921). System of mating.III. Assortative mating based on somatic resemblance. Genetics6, 144,161. Jérémie Nsengimana 1 , Ben D Brown 2 , Alistair S Hall 2 , Jenny H Barrett 141 Leeds Institute of Molecular Medicine, University of Leeds, UK 42 Leeds Institute for Genetics, Health and Therapeutics, University of Leeds, UK Keywords: Inflammatory genes, haplotype, coronary artery disease Genetic Risk of Acute Coronary Events (GRACE) is an initiative to collect cases of coronary artery disease (CAD) and their unaffected siblings in the UK and to use them to map genetic variants increasing disease risk. The aim of the present study was to test the association between CAD and 51 single nucleotide polymorphisms (SNPs) and their haplotypes from 35 inflammatory genes. Genotype data were available for 1154 persons affected before age 66 (including 48% before age 50) and their 1545 unaffected siblings (891 discordant families). Each SNP was tested for association to CAD, and haplotypes within genes or gene clusters were tested using FBAT (Rabinowitz & Laird, 2000). For the most significant results, genetic effect size was estimated using conditional logistic regression (CLR) within STATA adjusting for other risk factors. Haplotypes were assigned using HAPLORE (Zhang et al., 2005), which considers all parental mating types consistent with offspring genotypes and assigns them a probability of occurence. This probability was used in CLR to weight the haplotypes. In the single SNP analysis, several SNPs showed some evidence for association, including one SNP in the interleukin-1A gene. Analysing haplotypes in the interleukin-1 gene cluster, a common 3-SNP haplotype was found to increase the risk of CAD (P = 0.009). In an additive genetic model adjusting for covariates the odds ratio (OR) for this haplotype is 1.56 (95% CI: 1.16-2.10, p = 0.004) for early-onset CAD (before age 50). This study illustrates the utility of haplotype analysis in family-based association studies to investigate candidate genes. References Rabinowitz, D. & Laird, N. M. (2000) Hum Hered50, 211,223. Zhang, K., Sun, F. & Zhao, H. (2005) Bioinformatics21, 90,103. Andrea Foulkes 1 , Recai Yucel 1 , Xiaohong Li 143 Division of Biostatistics, University of Massachusetts, USA Keywords: Haploytpe, high-dimensional, mixed modeling The explosion of molecular level information coupled with large epidemiological studies presents an exciting opportunity to uncover the genetic underpinnings of complex diseases; however, several analytical challenges remain to be addressed. Characterizing the components to complex diseases inevitably requires consideration of synergies across multiple genetic loci and environmental and demographic factors. In addition, it is critical to capture information on allelic phase, that is whether alleles within a gene are in cis (on the same chromosome) or in trans (on different chromosomes.) In associations studies of unrelated individuals, this alignment of alleles within a chromosomal copy is generally not observed. We address the potential ambiguity in allelic phase in this high dimensional data setting using mixed effects models. Both a semi-parametric and fully likelihood-based approach to estimation are considered to account for missingness in cluster identifiers. In the first case, we apply a multiple imputation procedure coupled with a first stage expectation maximization algorithm for parameter estimation. A bootstrap approach is employed to assess sensitivity to variability induced by parameter estimation. Secondly, a fully likelihood-based approach using an expectation conditional maximization algorithm is described. Notably, these models allow for characterizing high-order gene-gene interactions while providing a flexible statistical framework to account for the confounding or mediating role of person specific covariates. The proposed method is applied to data arising from a cohort of human immunodeficiency virus type-1 (HIV-1) infected individuals at risk for therapy associated dyslipidemia. Simulation studies demonstrate reasonable power and control of family-wise type 1 error rates. Vivien Marquard 1 , Lars Beckmann 1 , Jenny Chang-Claude 144 Division of Cancer Epidemiology, German Cancer Research Center (DKFZ) Heidelberg, Germany Keywords: Genotyping errors, type I error, haplotype-based association methods It has been shown in several simulation studies that genotyping errors may have a great impact on the type I error of statistical methods used in genetic association analysis of complex diseases. Our aim was to investigate type I error rates in a case-control study, when differential and non-differential genotyping errors were introduced in realistic scenarios. We simulated case-control data sets, where individual genotypes were drawn from a haplotype distribution of 18 haplotypes with 15 markers in the APM1 gene. Genotyping errors were introduced following the unrestricted and symmetric with 0 edges error models described by Heid et al. (2006). In six scenarios, errors resulted from changes of one allele to another with predefined probabilities of 1%, 2.5% or 10%, respectively. A multiple number of errors per haplotype was possible and could vary between 0 and 15, the number of markers investigated. We examined three association methods: Mantel statistics using haplotype-sharing; a haplotype-specific score test; and Armitage trend test for single markers. The type I error rates were not influenced for any of all the three methods for a genotyping error rate of less than 1%. For higher error rates and differential errors, the type I error of the Mantel statistic was only slightly and of the Armitage trend test moderately increased. The type I error rates of the score test were highly increased. The type I error rates were correct for all three methods for non-differential errors. Further investigations will be carried out with different frequencies of differential error rates and focus on power. Arne Neumann 1 , Dörthe Malzahn 1 , Martina Müller 2 , Heike Bickeböller 145 Department of Genetic Epidemiology, Medical School, University of Göttingen, Germany 46 GSF-National Research Center for Environment and Health, Neuherberg & IBE-Institute of Epidemiology, Ludwig-Maximilians University München, Germany Keywords: Interaction, longitudinal, nonparametric Longitudinal data show the time dependent course of phenotypic traits. In this contribution, we consider longitudinal cohort studies and investigate the association between two candidate genes and a dependent quantitative longitudinal phenotype. The set-up defines a factorial design which allows us to test simultaneously for the overall gene effect of the loci as well as for possible gene-gene and gene time interaction. The latter would induce genetically based time-profile differences in the longitudinal phenotype. We adopt a non-parametric statistical test to genetic epidemiological cohort studies and investigate its performance by simulation studies. The statistical test was originally developed for longitudinal clinical studies (Brunner, Munzel, Puri, 1999 J Multivariate Anal 70:286-317). It is non-parametric in the sense that no assumptions are made about the underlying distribution of the quantitative phenotype. Longitudinal observations belonging to the same individual can be arbitrarily dependent on one another for the different time points whereas trait observations of different individuals are independent. The two loci are assumed to be statistically independent. Our simulations show that the nonparametric test is comparable with ANOVA in terms of power of detecting gene-gene and gene-time interaction in an ANOVA favourable setting. Rebecca Hein 1 , Lars Beckmann 1 , Jenny Chang-Claude 147 Division of Cancer Epidemiology, German Cancer Research Center (DKFZ) Heidelberg, Germany Keywords: Indirect association studies, interaction effects, linkage disequilibrium, marker allele frequency Association studies accounting for gene-environment interactions (GxE) may be useful for detecting genetic effects and identifying important environmental effect modifiers. Current technology facilitates very dense marker spacing in genetic association studies; however, the true disease variant(s) may not be genotyped. In this situation, an association between a gene and a phenotype may still be detectable, using genetic markers associated with the true disease variant(s) (indirect association). Zondervan and Cardon [2004] showed that the odds ratios (OR) of markers which are associated with the disease variant depend highly on the linkage disequilibrium (LD) between the variant and the markers, and whether the allele frequencies match and thereby influence the sample size needed to detect genetic association. We examined the influence of LD and allele frequencies on the sample size needed to detect GxE in indirect association studies, and provide tables for sample size estimation. For discordant allele frequencies and incomplete LD, sample sizes can be unfeasibly large. The influence of both factors is stronger for disease loci with small rather than moderate to high disease allele frequencies. A decline in D' of e.g. 5% has less impact on sample size than increasing the difference in allele frequencies by the same percentage. Assuming 80% power, large interaction effects can be detected using smaller sample sizes than those needed for the detection of main effects. The detection of interaction effects involving rare alleles may not be possible. Focussing only on marker density can be a limited strategy in indirect association studies for GxE. Cyril Dalmasso 1 , Emmanuelle Génin 2 , Catherine Bourgain 2 , Philippe Broët 148 JE 2492 , Univ. Paris-Sud, France 49 INSERM UMR-S 535 and University Paris Sud, Villejuif, France Keywords: Linkage analysis, Multiple testing, False Discovery Rate, Mixture model In the context of genome-wide linkage analyses, where a large number of statistical tests are simultaneously performed, the False Discovery Rate (FDR) that is defined as the expected proportion of false discoveries among all discoveries is nowadays widely used for taking into account the multiple testing problem. Other related criteria have been considered such as the local False Discovery Rate (lFDR) that is a variant of the FDR giving to each test its own measure of significance. The lFDR is defined as the posterior probability that a null hypothesis is true. Most of the proposed methods for estimating the lFDR or the FDR rely on distributional assumption under the null hypothesis. However, in observational studies, the empirical null distribution may be very different from the theoretical one. In this work, we propose a mixture model based approach that provides estimates of the lFDR and the FDR in the context of large-scale variance component linkage analyses. In particular, this approach allows estimating the empirical null distribution, this latter being a key quantity for any simultaneous inference procedure. The proposed method is applied on a real dataset. Arief Gusnanto 1 , Frank Dudbridge 150 MRC Biostatistics Unit, Cambridge UK Keywords: Significance, genome-wide, association, permutation, multiplicity Genome-wide association scans have introduced statistical challenges, mainly in the multiplicity of thousands of tests. The question of what constitutes a significant finding remains somewhat unresolved. Permutation testing is very time-consuming, whereas Bayesian arguments struggle to distinguish direct from indirect association. It seems attractive to summarise the multiplicity in a simple form that allows users to avoid time-consuming permutations. A standard significance level would facilitate reporting of results and reduce the need for permutation tests. This is potentially important because current scans do not have full coverage of the whole genome, and yet, the implicit multiplicity is genome-wide. We discuss some proposed summaries, with reference to the empirical null distribution of the multiple tests, approximated through a large number of random permutations. Using genome-wide data from the Wellcome Trust Case-Control Consortium, we use a sub-sampling approach with increasing density to estimate the nominal p-value to obtain family-wise significance of 5%. The results indicate that the significance level is converging to about 1e-7 as the marker spacing becomes infinitely dense. We considered the concept of an effective number of independent tests, and showed that when used in a Bonferroni correction, the number varies with the overall significance level, but is roughly constant in the region of interest. We compared several estimators of the effective number of tests, and showed that in the region of significance of interest, Patterson's eigenvalue based estimator gives approximately the right family-wise error rate. Michael Nothnagel 1 , Amke Caliebe 1 , Michael Krawczak 151 Institute of Medical Informatics and Statistics, University Clinic Schleswig-Holstein, University of Kiel, Germany Keywords: Association scans, Bayesian framework, posterior odds, genetic risk, multiplicative model Whole-genome association scans have been suggested to be a cost-efficient way to survey genetic variation and to map genetic disease factors. We used a Bayesian framework to investigate the posterior odds of a genuine association under multiplicative disease models. We demonstrate that the p value alone is not a sufficient means to evaluate the findings in association studies. We suggest that likelihood ratios should accompany p values in association reports. We argue, that, given the reported results of whole-genome scans, more associations should have been successfully replicated if the consistently made assumptions about considerable genetic risks were correct. We conclude that it is very likely that the vast majority of relative genetic risks are only of the order of 1.2 or lower. Clive Hoggart 1 , Maria De Iorio 1 , John Whittakker 2 , David Balding 152 Department of Epidemiology and Public Health, Imperial College London, UK 53 Department of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, UK Keywords: Genome-wide association analyses, shrinkage priors, Lasso Testing one SNP at a time does not fully realise the potential of genome-wide association studies to identify multiple causal variants of small effect, which is a plausible scenario for many complex diseases. Moreover, many simulation studies assume a single causal variant and so more complex realities are ignored. Analysing large numbers of variants simultaneously is now becoming feasible, thanks to developments in Bayesian stochastic search methods. We pose the problem of SNP selection as variable selection in a regression model. In contrast to single SNP tests this approach simultaneously models the effect of all SNPs. SNPs are selected by a Bayesian interpretation of the lasso (Tibshirani, 1996); the maximum a posterior (MAP) estimate of the regression coefficients, which have been given independent, double exponential prior distributions. The double exponential distribution is an example of a shrinkage prior, MAP estimates with shrinkage priors can be zero, thus all SNPs with non zero regression coefficients are selected. In addition to the commonly-used double exponential (Laplace) prior, we also implement the normal exponential gamma prior distribution. We show that use of the Laplace prior improves SNP selection in comparison with single -SNP tests, and that the normal exponential gamma prior leads to a further improvement. Our method is fast and can handle very large numbers of SNPs: we demonstrate its performance using both simulated and real genome-wide data sets with 500 K SNPs, which can be analysed in 2 hours on a desktop workstation. Mickael Guedj 1,2 , Jerome Wojcik 2 , Gregory Nuel 154 Laboratoire Statistique et Génome, Université d'Evry, Evry France 55 Serono Pharmaceutical Research Institute, Plan-les-Ouates, Switzerland Keywords: Local Replication, Local Score, Association In gene-mapping, replication of initial findings has been put forwards as the approach of choice for filtering false-positives from true signals for underlying loci. In practice, such replications are however too poorly observed. Besides the statistical and technical-related factors (lack of power, multiple-testing, stratification, quality control,) inconsistent conclusions obtained from independent populations might result from real biological differences. In particular, the high degree of variation in the strength of LD among populations of different origins is a major challenge to the discovery of genes. Seeking for Local Replications (defined as the presence of a signal of association in a same genomic region among populations) instead of strict replications (same locus, same risk allele) may lead to more reliable results. Recently, a multi-markers approach based on the Local Score statistic has been proposed as a simple and efficient way to select candidate genomic regions at the first stage of genome-wide association studies. Here we propose an extension of this approach adapted to replicated association studies. Based on simulations, this method appears promising. In particular it outperforms classical simple-marker strategies to detect modest-effect genes. Additionally it constitutes, to our knowledge, a first framework dedicated to the detection of such Local Replications. Juliet Chapman 1 , Claudio Verzilli 1 , John Whittaker 156 Department of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, UK Keywords: FDR, Association studies, Bayesian model selection As genomewide association studies become commonplace there is debate as to how such studies might be analysed and what we might hope to gain from the data. It is clear that standard single locus approaches are limited in that they do not adjust for the effects of other loci and problematic since it is not obvious how to adjust for multiple comparisons. False discovery rates have been suggested, but it is unclear how well these will cope with highly correlated genetic data. We consider the validity of standard false discovery rates in large scale association studies. We also show that a Bayesian procedure has advantages in detecting causal loci amongst a large number of dependant SNPs and investigate properties of a Bayesian FDR. Peter Kraft 157 Harvard School of Public Health, Boston USA Keywords: Gene-environment interaction, genome-wide association scans Appropriately analyzed two-stage designs,where a subset of available subjects are genotyped on a genome-wide panel of markers at the first stage and then a much smaller subset of the most promising markers are genotyped on the remaining subjects,can have nearly as much power as a single-stage study where all subjects are genotyped on the genome-wide panel yet can be much less expensive. Typically, the "most promising" markers are selected based on evidence for a marginal association between genotypes and disease. Subsequently, the few markers found to be associated with disease at the end of the second stage are interrogated for evidence of gene-environment interaction, mainly to understand their impact on disease etiology and public health impact. However, this approach may miss variants which have a sizeable effect restricted to one exposure stratum and therefore only a modest marginal effect. We have proposed to use information on the joint effects of genes and a discrete list of environmental exposures at the initial screening stage to select promising markers for the second stage [Kraft et al Hum Hered 2007]. This approach optimizes power to detect variants that have a sizeable marginal effect and variants that have a small marginal effect but a sizeable effect in a stratum defined by an environmental exposure. As an example, I discuss a proposed genome-wide association scan for Type II diabetes susceptibility variants based in several large nested case-control studies. Beate Glaser 1 , Peter Holmans 158 Biostatistics and Bioinformatics Unit, Cardiff University, School of Medicine, Heath Park, Cardiff, UK Keywords: Combined case-control and trios analysis, Power, False-positive rate, Simulation, Association studies The statistical power of genetic association studies can be enhanced by combining the analysis of case-control with parent-offspring trio samples. Various combined analysis techniques have been recently developed; as yet, there have been no comparisons of their power. This work was performed with the aim of identifying the most powerful method among available combined techniques including test statistics developed by Kazeem and Farrall (2005), Nagelkerke and colleagues (2004) and Dudbridge (2006), as well as a simple combination of ,2-statistics from single samples. Simulation studies were performed to investigate their power under different additive, multiplicative, dominant and recessive disease models. False-positive rates were determined by studying the type I error rates under null models including models with unequal allele frequencies between the single case-control and trios samples. We identified three techniques with equivalent power and false-positive rates, which included modifications of the three main approaches: 1) the unmodified combined Odds ratio estimate by Kazeem & Farrall (2005), 2) a modified approach of the combined risk ratio estimate by Nagelkerke & colleagues (2004) and 3) a modified technique for a combined risk ratio estimate by Dudbridge (2006). Our work highlights the importance of studies investigating test performance criteria of novel methods, as they will help users to select the optimal approach within a range of available analysis techniques. David Almorza 1 , M.V. Kandus 2 , Juan Carlos Salerno 2 , Rafael Boggio 359 Facultad de Ciencias del Trabajo, University of Cádiz, Spain 60 Instituto de Genética IGEAF, Buenos Aires, Argentina 61 Universidad Nacional de La Plata, Buenos Aires, Argentina Keywords: Principal component analysis, maize, ear weight, inbred lines The objective of this work was to evaluate the relationship among different traits of the ear of maize inbred lines and to group genotypes according to its performance. Ten inbred lines developed at IGEAF (INTA Castelar) and five public inbred lines as checks were used. A field trial was carried out in Castelar, Buenos Aires (34° 36' S , 58° 39' W) using a complete randomize design with three replications. At harvest, individual weight (P.E.), diameter (D.E.), row number (N.H.) and length (L.E.) of the ear were assessed. A principal component analysis, PCA, (Infostat 2005) was used, and the variability of the data was depicted with a biplot. Principal components 1 and 2 (CP1 and CP2) explained 90% of the data variability. CP1 was correlated with P.E., L.E. and D.E., meanwhile CP2 was correlated with N.H. We found that individual weight (P.E.) was more correlated with diameter of the ear (D.E.) than with length (L.E). Five groups of inbred lines were distinguished: with high P.E. and mean N.H. (04-70, 04-73, 04-101 and MO17), with high P.E. but less N.H. (04-61 and B14), with mean P.E. and N.H. (B73, 04-123 and 04-96), with high N.H. but less P.E. (LP109, 04-8, 04-91 and 04-76) and with low P.E. and low N.H. (LP521 and 04-104). The use of PCA showed which variables had more incidence in ear weight and how is the correlation among them. Moreover, the different groups found with this analysis allow the evaluation of inbred lines by several traits simultaneously. Sven Knüppel 1 , Anja Bauerfeind 1 , Klaus Rohde 162 Department of Bioinformatics, MDC Berlin, Germany Keywords: Haplotypes, association studies, case-control, nuclear families The area of gene chip technology provides a plethora of phase-unknown SNP genotypes in order to find significant association to some genetic trait. To circumvent possibly low information content of a single SNP one groups successive SNPs and estimates haplotypes. Haplotype estimation, however, may reveal ambiguous haplotype pairs and bias the application of statistical methods. Zaykin et al. (Hum Hered, 53:79-91, 2002) proposed the construction of a design matrix to take this ambiguity into account. Here we present a set of functions written for the Statistical package R, which carries out haplotype estimation on the basis of the EM-algorithm for individuals (case-control) or nuclear families. The construction of a design matrix on basis of estimated haplotypes or haplotype pairs allows application of standard methods for association studies (linear, logistic regression), as well as statistical methods as haplotype sharing statistics and TDT-Test. Applications of these methods to genome-wide association screens will be demonstrated. Manuela Zucknick 1 , Chris Holmes 2 , Sylvia Richardson 163 Department of Epidemiology and Public Health, Imperial College London, UK 64 Department of Statistics, Oxford Center for Gene Function, University of Oxford, UK Keywords: Bayesian, variable selection, MCMC, large p, small n, structured dependence In large-scale genomic applications vast numbers of markers or genes are scanned to find a few candidates which are linked to a particular phenotype. Statistically, this is a variable selection problem in the "large p, small n" situation where many more variables than samples are available. An additional feature is the complex dependence structure which is often observed among the markers/genes due to linkage disequilibrium or their joint involvement in biological processes. Bayesian variable selection methods using indicator variables are well suited to the problem. Binary phenotypes like disease status are common and both Bayesian probit and logistic regression can be applied in this context. We argue that logistic regression models are both easier to tune and to interpret than probit models and implement the approach by Holmes & Held (2006). Because the model space is vast, MCMC methods are used as stochastic search algorithms with the aim to quickly find regions of high posterior probability. In a trade-off between fast-updating but slow-moving single-gene Metropolis-Hastings samplers and computationally expensive full Gibbs sampling, we propose to employ the dependence structure among the genes/markers to help decide which variables to update together. Also, parallel tempering methods are used to aid bold moves and help avoid getting trapped in local optima. Mixing and convergence of the resulting Markov chains are evaluated and compared to standard samplers in both a simulation study and in an application to a gene expression data set. Reference Holmes, C. C. & Held, L. (2006) Bayesian auxiliary variable models for binary and multinomial regression. Bayesian Analysis1, 145,168. Dawn Teare 165 MMGE, University of Sheffield, UK Keywords: CNP, family-based analysis, MCMC Evidence is accumulating that segmental copy number polymorphisms (CNPs) may represent a significant portion of human genetic variation. These highly polymorphic systems require handling as phenotypes rather than co-dominant markers, placing new demands on family-based analyses. We present an integrated approach to meet these challenges in the form of a graphical model, where the underlying discrete CNP phenotype is inferred from the (single or replicate) quantitative measure within the analysis, whilst assuming an allele based system segregating through the pedigree. [source] Arsenic speciation in terrestrial birds from Yellowknife, Northwest Territories, Canada: The unexpected finding of arsenobetaineENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 6 2005Iris Koch Abstract The surrounding area of Yellowknife, Northwest Territories, Canada, is known for naturally and anthropogenically elevated concentrations of arsenic. Five bird species (gray jay [Perisoreus canadensis], American tree sparrow [Spizella arborea], dark-eyed junco [Junco hyemalis], yellow-rumped warbler [Dendroica coronata], and spruce grouse [Dendragapus canadensis]) were collected from this area. Their tissues were analyzed for total arsenic and for arsenic species, allowing us to report, to our knowledge for the first time, the arsenic characterization in terrestrial birds. Total arsenic concentrations were determined in the terrestrial birds by inductively coupled plasma-optical emission spectrometry, whereas arsenic speciation analysis was performed using high-performance liquid chromatography-inductively coupled plasma-mass spectrometry. Total arsenic concentrations were substantially higher in the terrestrial bird species studied from Yellowknife compared with those reported previously in the literature. The primary arsenic species detected in two of the bird species studied was arsenobetaine. Normally, arsenobetaine is not formed or retained by terrestrial animals. Thus, the birds in the present study were thought to be highly adapted compared with other terrestrial animals, because they were able to form and/or retain this relatively nontoxic arsenic compound. This adaptation is thought to be a consequence of the elevated concentrations of arsenic in the Yellowknife area. [source] Experimental Manipulation of Intraclutch Variation in the Great Reed Warbler Shows No Effect on Rejection of Parasitic EggsETHOLOGY, Issue 1 2003Zsolt Karcza In the continuing arms race between hosts and brood parasites, hosts are expected to reduce variation in the appearance of their own eggs within clutches, as it facilitates recognition of parasitic eggs. At the same time, by increasing interclutch variation, hosts should make it more difficult for parasites to evolve perfectly mimetic eggs. In this study, we experimentally manipulated intraclutch variation in the great reed warbler, Acrocephalus arundinaceus, in Hungary, where this species is heavily (c. 64%) parasitized by the common cuckoo, Cuculus canorus. We placed artificial cuckoo eggs, which appeared moderately mimetic to humans, in two groups of nests; in one group we increased variability of egg appearance within clutches by exchanging host eggs among nests. These clutches showed a significantly higher intraclutch variability than natural clutches, which we used as a control group. Our results indicate that it has no effect on rejection behaviour in this species, neither when variation was increased experimentally, nor within the natural range of variation displayed by our population. We suggest that when parasitism is high, selection for reduced intraclutch variation may be less important than frequency-dependent selection for increased variation between individuals within a host population. [source] INCIPIENT SPECIATION DESPITE LITTLE ASSORTATIVE MATING: THE YELLOW-RUMPED WARBLER HYBRID ZONEEVOLUTION, Issue 12 2009Alan Brelsford Hybrid zones between recently diverged taxa are natural laboratories for speciation research, allowing us to determine whether there is reproductive isolation between divergent forms and the causes of that isolation. We present a study of a classic avian hybrid zone in North America between two subspecies of the yellow-rumped warbler (Dendroica coronata). Although previous work has shown very little differentiation in mitochondrial DNA across this hybrid zone, we identified two nuclear loci (one sex-linked and one autosomal) that show fixed differences across the hybrid zone, in a close concordance with patterns of plumage variation. Temporal stability and limited width of the hybrid zone, along with substantial linkage disequilibrium between these two diagnostic markers in the center of the zone, indicate that there is moderate reproductive isolation between these populations, with an estimated strength of selection maintaining the zone of 18%. Pairing data indicate that assortative mating is either very weak or absent, suggesting that this reproductive isolation is largely due to postmating barriers. Thus, despite extensive hybridization the two forms are distinct evolutionary groups carrying genes for divergent adaptive peaks, and this situation appears relatively stable. [source] INBREEDING IN THE SEYCHELLES WARBLER: ENVIRONMENT-DEPENDENT MATERNAL EFFECTSEVOLUTION, Issue 9 2004David S. Richardson Abstract The deleterious effects of inbreeding can be substantial in wild populations and mechanisms to avoid such matings have evolved in many organisms. In situations where social mate choice is restricted, extrapair paternity may be a strategy used by females to avoid inbreeding and increase offspring heterozygosity. In the cooperatively breeding Seychelles warbler, Acrocephalus sechellensis, neither social nor extrapair mate choice was used to avoid inbreeding facultatively, and close inbreeding occurred in approximately 5% of matings. However, a higher frequency of extra-group paternity may be selected for in female subordinates because this did reduce the frequency of mating between close relatives. Inbreeding resulted in reduced individual heterozygosity, which, against expectation, had an almost significant (P= 0.052), positive effect on survival. Conversely, low heterozygosity in the genetic mother was linked to reduced offspring survival, and the magnitude of this intergenerational inbreeding depression effect was environment-dependent. Because we controlled for genetic effects and most environmental effects (through the experimental cross-fostering of nestlings), we conclude that the reduced survival was a result of maternal effects. Our results show that inbreeding can have complicated effects even within a genetic bottlenecked population where the "purging" of recessive alleles is expected to reduce the effects of inbreeding depression. [source] SONG VARIATION IN AN AVIAN RING SPECIESEVOLUTION, Issue 3 2000Darren E. Irwin Abstract., Divergence of mating signals can occur rapidly and be of prime importance in causing reproductive isolation and speciation. A ring species, in which two reproductively isolated taxa are connected by a chain of intergrading populations, provides a rare opportunity to use spatial variation to reconstruct the history of divergence. I use geographic variation in the song of a likely ring species, the greenish warbler (Phylloscopus trochiloides) to reconstruct the microevolutionary steps that occurred during divergence of a trait that is often important in speciation in birds. Populations of a western Siberian (P. t. viridanus) and an eastern Siberian (P. t. plumbeitarsus) form of the greenish warbler meet, but do not interbreed in central Siberia; these forms are connected by a chain of interbreeding populations extending in a ring to the south around the treeless Tibetan Plateau. I show that: (1) song structure differs greatly between the two Siberian forms, which share the same habitat; (2) song structure changes gradually around the ring; (3) singing behavior is relatively simple in the Himalayas, but becomes increasingly complex to the north, both to the west and east of the Tibetan Plateau; and (4) song varies along independent axes of complexity in the western and eastern south-north clines. By comparing geographic variation in singing behavior and ecological variables, I distinguish among possible causes of song divergence, including selection based on the acoustic environment, stochastic effects of sexual selection, and selection for species recognition. I suggest that parallel south-to-north ecological gradients have caused a greater intensity of sexual selection on song in northern populations and that the stochastic effects of sexual selection have led to divergence in song structure. [source] Carotenoid and melanin-based ornaments signal similar aspects of male quality in two populations of the common yellowthroatFUNCTIONAL ECOLOGY, Issue 1 2010Peter O. Dunn Summary 1.,Female preferences for particular male ornaments may shift between populations as a consequence of ecological differences that change the reliability and detectability of the ornament, but few studies have examined how ornaments function in different populations. 2.,We examined the signalling function of male plumage ornaments in a warbler, the common yellowthroat (Geothlypis trichas), breeding in New York (NY) and Wisconsin (WI), USA. Males have two prominent ornaments: a black facial mask pigmented with melanin and a yellow bib pigmented by carotenoids. Previous studies in WI indicate that the size of the mask, and not the bib, is primarily related to female choice and male reproductive success. In NY, however, the pattern is reversed and attributes of the bib (size and colour), and not the mask, are the target of sexual selection. 3.,We found that brightness of the yellow bib was the best signal of humoral immunity (immunoglobulin G) in NY and mask size was the best signal in WI, after controlling for breeding experience and capture date. Thus, similar aspects of male quality appeared to be signalled by different ornaments in different populations. 4.,There was no difference between populations in the level of plasma carotenoids or the prevalence of malarial parasites, which may affect the costs and benefits of choosing males with particular ornaments in each location. 5.,Even though females in different populations prefer different ornaments produced by different types of pigments, these ornaments appear to be signalling similar aspects of male quality. Our results caution against inferring the function of particular ornaments based simply on their type of pigment. [source] Examining the total arrival distribution of migratory birdsGLOBAL CHANGE BIOLOGY, Issue 1 2005T. H. Sparks Abstract This paper reports on the total distribution of spring migration timing of willow warbler, chiffchaff and pied flycatcher at locations in the UK, Germany, Russia and Finland. This is the first time that high-quality data based on known-effort monitoring has been examined on a continental scale. First arrival dates, commonly reported in the literature, were positively correlated with mean arrival dates although they would not make good predictors of the latter. At all locations, at least one aspect of the arrival distribution of each species had got significantly earlier in recent years. The trend towards earliness was associated with warmer local temperatures and more positive winter North Atlantic Oscillation index. In years that were early, the arrival distribution became more elongated and skewed. Researchers should now investigate the consequences of earlier arrival on current and future bird populations. [source] The role of group size and environmental factors on survival in a cooperatively breeding tropical passerineJOURNAL OF ANIMAL ECOLOGY, Issue 6 2006LYANNE BROUWER Summary 1Variation in survival, a major determinant of fitness, may be caused by individual or environmental characteristics. Furthermore, interactions between individuals may influence survival through the negative feedback effects of density dependence. Compared to species in temperate regions, we have little knowledge about population processes and variation in fitness in tropical bird species. 2To investigate whether variation in survival could be explained by population size or climatic variables we used capture,recapture models in conjunction with a long-term data set from an island population of the territorial, cooperatively breeding Seychelles warbler (Acrocephalus sechellensis). The lack of migration out of the study population means that our results are not confounded by dispersal. 3Annual survival was high, both for adults (84%) and juveniles (61%), and did not differ between the sexes. Although there was significant variation in survival between years, this variation could not be explained by overall population size or weather variables. 4For territorial species, resource competition will work mainly on a local scale. The size of a territory and number of individuals living in it will therefore be a more appropriate measure of density than overall population density. Consequently, both an index of territory quality per individual (food availability) and local density, measured as group size, were included as individual covariates in our analyses. 5Local density had a negative effect on survival; birds living in larger groups had lower survival probabilities than those living in small groups. Food availability did not affect survival. 6Our study shows that, in a territorial species, although density-dependent effects might not be detectable at the population level they can be detected at the individual territory level , the scale at which individuals compete. These results will help to provide a better understanding of the small-scale processes involved in the dynamics of a population in general, but in particular in tropical species living in relatively stable environments. [source] Geographic variation in the function of ornaments in the common yellowthroat Geothlypis trichasJOURNAL OF AVIAN BIOLOGY, Issue 1 2008Peter O. Dunn We used controlled aviary experiments to study the role of male ornaments in male-male competition and female choice in the common yellowthroat Geothlypis trichas, a sexually dichromatic warbler. Previous aviary studies in Wisconsin, USA, indicated that males with larger black facial masks were dominant over males with smaller masks and preferred by females in mate choice experiments. In this study, we replicated those experiments in a population in New York, USA, where male mating success was related more consistently to the size of the yellow bib (throat, breast, and belly) than to the size of the mask. Similar to the study in Wisconsin, we found that males with larger masks were more likely to be dominant in New York, however, we found that males with larger bibs were preferred by females in New York, and there was no significant preference for males with larger masks. These results are consistent with the hypothesis that carotenoid-based ornaments are selected by female choice and melanin-based ornaments are selected by male-male competition. However, the pattern of female choice appears to vary between New York and Wisconsin. This geographic difference could be related to a variety of environmental factors (habitat, carotenoid and parasite abundance) that affect the costs and benefits of choosing males with particular ornaments in each location. [source] Differential migration of chiffchaffs Phylloscopus collybita and P. ibericus in Europe and AfricaJOURNAL OF AVIAN BIOLOGY, Issue 3 2005Paulo Catry Differential migration is a widespread, but poorly understood, phenomenon in birds. In this paper, we present the first detailed field study of differential migration in the Old World warbler (Sylviidae) family. We studied two chiffchaff Phylloscopus [collybita] semispecies: the common chiffchaff P. [c.] collybita and the Iberian chiffchaff P. [c.] ibericus. Using data collected at several latitudes in Europe and Africa, we present convincing evidence for differential distance migration of sexes in chiffchaffs, with females moving further than males. Interestingly, while there was a pronounced gradient in the sex-ratios in Europe and North Africa (with an increasing proportion of females with declining latitude), no clear pattern was found south of the Sahara, where sex-ratios were more male-biased than predicted by a simple latitude model. This suggests that, amongst the chiffchaffs wintering in West Africa, a large proportion is composed by Iberian birds, and provides support to previous suggestions that Iberian chiffchaffs are long distance migrants. Results from detailed studies in Senegal also show that chiffchaffs display differential timing of spring migration, with males leaving the winter quarters considerably earlier than females. The results are discussed in the framework of the three main (non-mutually exclusive) hypotheses attempting to explain the latitudinal segregation of the sexes. Given the relative failure of standard comparative studies to discriminate between competing single-factor hypotheses to explain differential migration, it is argued that the chiffchaff species complex might be particularly suited to study this issue using a new approach suggested by Cristol et al. (1999): detailed (further) comparisons between closely related species (such as the common and the Iberian chiffchaffs) could help identifying the key factors to be incorporated into optimality models that can predict relative distance of migration of different sex or age classes. [source] Breeding success of common cuckoos Cuculus canorus parasitising four sympatric species of Acrocephalus warblersJOURNAL OF AVIAN BIOLOGY, Issue 5 2004Oddmund Kleven We investigated the level of parasitism, egg mimicry and breeding success of cuckoos parasitising four sympatric species of Acrocephalus warblers in southern Moravia, Czech Republic. The parasitism rate was highest in the marsh warbler Acrocephalus palustris (44.8%) followed by great reed warbler A. arundinaceus (33.8%), sedge warbler A. schoenobaenus (26.5%) and reed warbler A. scirpaceus (11.6%). Although the cuckoo eggs showed a high level of mimicry the eggs of the marsh warbler this host species rejected 72% of the cuckoo eggs, resulting in a cuckoo breeding success of only 4.3%. Cuckoo eggs laid in great reed warbler and reed warbler nests showed a similar hatching success, but the cuckoo chicks survived better in great reed warbler nests, resulting in a breeding success of 30.4%, as compared to 16.4% in nests of the reed warbler. The relationship between the level of parasitism, host rejection of cuckoo eggs, cuckoo chick survival and breeding success is discussed for the four host species. [source] Range expansion of the globally Vulnerable Karamoja apalis Apalis karamojae in the Serengeti ecosystemAFRICAN JOURNAL OF ECOLOGY, Issue 3 2010Philip Shaw Abstract The underlying causes of change in geographic range size are less well understood in African birds than in north temperate species. Here, we examine factors associated with range expansion in the Karamoja apalis (Apalis karamojae), a globally Vulnerable warbler confined to north-east Uganda, north-central Tanzania and southern Kenya. In Tanzania, it was originally known only from the Wembere Steppe, but since 1993 (and possibly as early as 1983) has extended its range into the Serengeti ecosystem, c. 140 km to the north, reaching southern Kenya by 2004. Changes in the warbler's range within the Serengeti have broadly reflected a cyclical change in the density of its main habitat, Acacia drepanolobium woodland, which was low in the 1970s, high during the 1980s and 1990s, and declined in the early 2000s. Karamoja apalis records in the Serengeti showed a 5 year time lag behind A. drepanolobium density, which was in turn negatively correlated with the area of grassland burnt 10 years earlier. Previous studies in the Serengeti have also linked Acacia regeneration to changes in grazing pressure, as increasing wildebeest (Connochaetes taurinus) numbers have reduced the volume of combustible material present, and hence the frequency of damaging ,hot burns'. We conclude that this globally threatened warbler appears to have benefited from changes in ungulate populations in the Serengeti, which have influenced burning intensity and hence tree regeneration. The warbler's range now appears to be declining, however, following a recent reduction in the density and annual survival of A. drepanolobium in the northern Serengeti. Résumé Les causes sous-jacentes du changement de la taille d'une distribution géographique sont moins bien connues pour les oiseaux africains que pour les espèces du nord tempéré. Nous examinons ici des facteurs liés à l'expansion de l'aire de répartition de l'apalis de Karamoja Apalis karamojae, un sylviidé classé comme Vulnérable au niveau mondial, confiné au NE de l'Ouganda, au centre-nord de la Tanzanie et au sud du Kenya. En Tanzanie, on ne le connaissait à l'origine que dans la steppe de Wembere mais depuis 1993, et peut-être même dès 1983, il a étendu son aire de répartition dans l'écosystème du Serengeti, environ 140 km plus au nord, et atteint le sud du Kenya en 2004. Les changements de l'aire de répartition de ce sylviidé dans le Serengeti reflètent largement un changement cyclique de la densité de son habitat principal, la forêt d'Acacia drepanolobium, qui était faible dans les années 1970, forte pendant les années 1980 et 1990, et qui a diminué au début des années 2000. Les rapports sur l'apalis de Karamoja au Serengeti montrent un retard de cinq ans par rapport à l'évolution de la densité d'A. drepanolobium, elle-même étant négativement liée à la zone de prairie brûlée 10 ans plus tôt. Des études antérieures faites au Serengeti lient aussi la régénération des acacias aux changements de la pression du pâturage, étant donné que le nombre croissant de gnous, Connochaetes taurinus, a réduit le volume des matières combustibles restantes et donc la fréquence des feux trop chauds qui causent beaucoup de dégâts. Nous concluons que cet oiseau menacé au niveau mondial semble avoir bénéficié des changements des populations d'ongulés au Serengeti, qui ont influencé l'intensité des feux et donc la régénération des arbres. L'aire de répartition de ce sylviidé semble pourtant en train de se réduire suite à une récente réduction de la densité et de la survie annuelle d'A. drepanolobium dans le nord du Serengeti. [source] Genetic divergence and migration patterns in a North American passerine bird: implications for evolution and conservationMOLECULAR ECOLOGY, Issue 8 2006LESLIE A. DAVIS Abstract Like many other migratory birds, the black-throated blue warbler (Dendroica caerulescens) shows pronounced differences in migratory behaviour and other traits between populations: birds in the southern part of the breeding range have darker plumage and migrate to the eastern Caribbean during the winter, whereas those in the north have lighter plumage and migrate to the western Caribbean. We examined the phylogeography of this species, using samples collected from northern and southern populations, to determine whether differentiation between these populations dates to the Pleistocene or earlier, or whether differences in plumage and migratory behaviour have arisen more recently. We analysed variation at 369 bp of the mitochondrial control region domain I and also at seven nuclear microsatellites. Analyses revealed considerable genetic variation, but the vast majority of this variation was found within rather than between populations, and there was little differentiation between northern and southern populations. Phylogeographic analyses revealed a very shallow phylogenetic tree, a star-like haplotype network, and a unimodal mismatch distribution, all indicative of a recent range expansion from a single refugium. Coalescent modelling approaches also indicated a recent common ancestor for the entire group of birds analysed, no split between northern and southern populations, and high levels of gene flow. These results show that Pleistocene or earlier events have played little role in creating differences between northern and southern populations, suggesting that migratory and other differences between populations have arisen very recently. The implications of these results for the evolution of migration and defining taxonomic groups for conservation efforts are discussed. [source] Phylogeography and genetic structure of northern populations of the yellow warbler (Dendroica petechia)MOLECULAR ECOLOGY, Issue 6 2000Emmanuel Milot Abstract Phylogeographic patterns of intraspecific variation can provide insights into the population-level processes responsible for speciation and yield information useful for conservation purposes. To examine phylogeography and population structure in a migratory passerine bird at both continental and regional geographical scales, we analysed 344 bp of mitochondrial DNA (mtDNA) control region sequence from 155 yellow warblers (Dendroica petechia) collected from seven locations across Canada and from Alaska. There is a major subdivision between eastern (Manitoba to Newfoundland) and western (Alaska and British Columbia) populations which appears to have developed during the recent Pleistocene. Some localities within these two regions also differ significantly in their genetic composition, suggesting further subdivision on a regional geographical scale. Eastern and western birds form distinct phylogeographic entities and the clustering of all western haplotypes with two eastern haplotypes suggests that the western haplotypes may be derived from an eastern lineage. Analyses based on coalescent models support this explanation for the origin of western haplotypes. These results are consistent with important features of Mengel's model of warbler diversification. From a conservation perspective they also suggest that individual populations of migrant birds may form demographically isolated management units on a smaller scale than previously appreciated. [source] Begging call matching between a specialist brood parasite and its host: a comparative approach to detect coevolutionBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009MICHAEL G. ANDERSON Studies of avian brood parasite systems have typically investigated the mimicry of host eggs by specialist parasites. Yet, several examples of similarity between host and parasite chick appearance or begging calls suggest that the escalation of host,parasite arms races may also lead to visual or vocal mimicry at the nestling stage. Despite this, there have been no large-scale comparative studies of begging calls to test whether the similarity of host and parasite is greater than predicted by chance or phylogenetic distance within a geographically distinct species assemblage. Using a survey of the begging calls of all native forest passerines in New Zealand, we show that the begging call of the host-specialist shining cuckoo (Chrysococcyx lucidus) is most similar to that of its grey warbler (Gerygone igata) host compared to any of the other species, and that this is unlikely to have occurred by chance. Randomization tests revealed that the incorporation of the shining cuckoo's begging calls into our species-set consistently reduced the phylogenetic signal within cluster trees based on begging call similarity. By contrast, the removal of the grey warbler calls did not reduce the phylogenetic signal in the begging call similarity trees. These two results support a scenario in which coevolution of begging calls has not taken place: the begging call of the host retains its phylogenetic signal, whereas that of the parasite has changed to match that of its host. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 208,216. [source] Accumulation of DDT and mercury in prothonotary warblers (Protonotaria citrea) foraging in a heterogeneously contaminated environmentENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 12 2001Kevin D. Reynolds Abstract Foraging areas of adult prothonotary warblers (Protonotaria citrea) were determined using standard radiotelemetry techniques to determine if soil concentrations of p,p,dichlorodiphenyltrichloroethane (p,p,DDT) and mercury in foraging areas could be used to predict contaminant levels in diets and tissues of nestling warblers. Adult warblers were fitted with transmitters and monitored for approximately 2 d while foraging and feeding 6- to 8-d-old nestlings. Foraging ecology data were integrated with contaminant levels of soil, diets, and tissues into a comprehensive analysis of geographic variation in contaminant exposure and uptake using linear regression. Concentrations of 1,1-dichloro-2,2-bis(p -chlorophenyl)ethylene (DDE) and mercury in nestling tissues varied considerably across the study site. Mean concentration of DDE was greater in eggs than all other tissues, with individual samples ranging from 0.24 to 8.12 ,g/kg. In general, concentrations of DDT in soil were effective in describing the variation of contaminants in adipose samples. Concentrations of mercury in soils accounted for 78% of the variation in kidney samples. This was the best relationship of any of the paired variables. All other relationships showed relatively poor predictive ability. [source] Enemy Recognition of Reed Warblers (Acrocephalus scirpaceus): Threats and Reproductive Value Act Independently in Nest Defence ModulationETHOLOGY, Issue 6 2010Daniela Campobello Organisms should respond more aggressively towards species perceived as a danger to their offspring, but intensity of defence may be gauged by the value of current offspring weighed against the value of future reproductive opportunities. We tested whether defensive responses of nesting reed warblers (Acrocephalus scirpaceus) are the result of an interaction effect between the type of stimulus confronted and the value of the warbler's nesting attempt. We quantified the ability of reed warblers to discriminate among brood parasites, nestling predators and non-threatening species at different stages of the breeding cycle. We also determined whether variables that influence the value of offspring, such as time of season, size and age of clutch or brood, and time of day and number of visits to the nest, explain variation in the intensity of defence recorded during the egg and nestling stages. Responses to the three stimuli differed significantly, as reed warblers consistently directed their mobbing calls and attacks towards parasites, whereas they were less conspicuous when confronted with models of predators. Reed warblers modulated their responses towards each stimulus in accordance with the threat each posed at a specific nesting stage, whereas they were not affected by other variables relative to their reproductive potential. The churr call, however, was uttered independently of the stimulus, as it was triggered by the mere presence of nestlings in the nest. [source] Variation in Vocal Performance in the Songs of a Wood-Warbler: Evidence for the Function of Distinct Singing ModesETHOLOGY, Issue 7 2004Martin D. Beebee Male North American wood-warblers (family Parulidae) subdivide their song repertoires into two different categories, or modes, of singing (first and second category songs). These two modes are thought to be specialized for interacting with females and males, although the data are inconclusive. I conducted an acoustic analysis of the song types used by yellow warblers (Dendroica petechia) for type I (first category) and type II (second category) singing to ask whether there are consistent structural differences between them which could provide insight into how they might function as separate signals. I found that type I songs are performed closer to the upper boundary of a song performance limit, measured in terms of the difficulty of production, compared with type II songs. By contrast, the performance of specific song types did not depend on whether they were used for type I singing vs. type II singing by different males. In addition, type I songs had a greater amplitude increase across the first two syllables compared with type II songs. There was no relationship between the performance of type I or type II songs and male condition. These results suggest that wood-warblers might subdivide their song repertoire into distinct categories to highlight the relative vocal performance of their songs. [source] Islands in a desert: breeding ecology of the African Reed Warbler Acrocephalus baeticatus in NamibiaIBIS, Issue 4 2001CORINE M. EISING The continental African Reed Warbler Acrocephalus baeticatus, like its relative the Seychelles Warbler Acrocephalus sechellensis, breeds in isolated patches. We studied the mating system of the African Reed Warbler to see whether this species, like the Seychelles Warbler, shows co-operative breeding. The African Reed Warbler is not polygynous. The majority breed monogamously (88%, n= 65), however in 12% of the territories three adult unrelated birds (mostly males) were observed participating in the brooding and feeding of nestlings, suggesting a polyandrous breeding system. Multilocus DNA fingerprinting revealed that the helping bird was unrelated to the pair birds. The percentage of nests with helpers was low compared to rates found in the Seychelles Warbler or Henderson Reed Warbler Acrocephalus vaughani taiti. This could be due to the scarcity of potential helpers or to the fact that, although limited, birds still had the opportunity to disperse within a meta-population structure in search of vacant territories. The presence of helpers was associated with increased hatching success due to lower predation rates, but not with increased fledging success. Another possible benefit of helping behaviour in this species could be improved predator detection and mobbing. Nest predation was high and warblers tended to build their nests in the highest, most dense reed patches available in their territory. There was no relation between habitat quality, measured as insect food availability, and the occurrence of helpers. [source] Effects of food availability on the distribution of migratory warblers among habitats in JamaicaJOURNAL OF ANIMAL ECOLOGY, Issue 4 2001Matthew D. Johnson Summary 1Theoretical arguments suggest that distributions of migratory birds in winter should match patterns of food availability, but in reality the match between migrants and their food may be imperfect because, for various reasons, birds may be unable to ,track' food resources. We tested the hypothesis that food availability influences the distribution of migratory canopy-foraging insectivorous warblers wintering in Jamaica. 2Over a wide spatial scale (24 sites on the island), warbler abundance varied significantly among sites and habitats and was significantly dependent on measures of arthropod biomass. Alternative factors (vegetation characteristics, resident bird competitor abundance, predator abundance) were not correlated with warbler abundance. 3Over a short temporal scale (about 2 weeks) at a single site, warbler abundance increased as predicted quantitatively after a natural, rapid increase in arthropod biomass. 4Over a longer temporal scale (the duration of a winter), changes in density and persistence of individually marked American redstarts (Setophaga ruticilla, L.) on six sites corresponded with concurrent fluctuations in arthropod biomass. 5These results document a strong association between arthropod biomass and warbler abundance in time and space, suggesting that warblers wintering in Jamaica distribute themselves in response to food resources. 6We hypothesize that dominance hierarchies and variable movement strategies operate in concert with birds' responses to food to influence the distribution of wintering warblers at different spatial scales. Whether food availability determines habitat quality remains to be investigated. [source] Breeding latitude and timing of spring migration in songbirds crossing the Gulf of MexicoJOURNAL OF AVIAN BIOLOGY, Issue 3 2009Kathryn M. Langin Each spring, millions of songbirds migrate across the Gulf of Mexico on their way to breeding sites in North America. Data from radar and migration monitoring stations have revealed broad patterns in the spatial and temporal course of trans-Gulf migration. Unfortunately, we have limited information on where these birds have previously spent the winter and where they are migrating to breed. Here we measure stable-hydrogen isotopes in feathers (,Df) to infer the breeding latitude of five species of songbirds , hooded warblers Wilsonia citrina, American redstarts Setophaga ruticilla, black-and-white warblers Mniotilta varia, ovenbirds Seiurus aurocapilla, and northern waterthrushes S. noveboracensis, that were captured at a stopover site along the coast of southwestern Louisiana in spring 2004. Values of ,Df across all species ranged from ,163 to ,35, (n=212), and within most species the range was consistent with the latitudinal extent of known breeding sites in central and eastern North America. Individuals that arrived first along the northern Gulf coast had ,Df values indicative of southerly breeding sites in hooded warblers, American redstarts, black-and-white warblers, and ovenbirds, but no relationship was found between passage timing and ,Df for northern waterthrushes. Our findings suggest that spring passage is often timed to coincide with the emergence of suitable conditions on breeding areas, with southern breeding birds migrating first. [source] Nestling sex ratio of golden-winged warblers Vermivora chrysoptera in an introgressed populationJOURNAL OF AVIAN BIOLOGY, Issue 6 2008Kate J. Neville Sex ratio biases in avian species remain controversial, although several studies have documented apparent facultative adjustment of offspring sex ratios. While hybridizing pied and collared flycatchers have exhibited sex ratio skews that may be a response to sex-based costs associated with hybridization, this appears not to be true of a hybridized population of blue-winged Vermivora pinus and golden-winged V. chrysoptera warblers. We examined the primary sex ratio of nestlings in a population of hybrid and introgressed golden-winged warblers. The sex ratio of 298 nestlings from 81 nests in the population was approximately 50:50. We conducted paternity assignments and analyzed groups of nestlings with shared genetic parents ("genetic broods") and found no difference from the expected binomial distribution, and no statistically significant relationship between parental species phenotype and nestling sex ratio. We saw no evidence of preferential production of male or female nestlings, and female hybrids were found to mate and breed in the population. This suggests that heterogametic (female) hybrids are both viable and fertile, and thus that Haldane's Rule does not apply to this system. While populations of hybridizing golden-winged warblers should be monitored for evidence of costs of heterospecific pairings, it is unlikely that adjustment of sex ratios would be the form of compensation for sub-optimal mating conditions. Our results provide support for the emerging hypothesis that hybrids suffer no disadvantage relative to golden-winged and blue-winged warblers. [source] | |||||||||||||||||||||||||||||||