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Extensive Sampling (extensive + sampling)
Selected AbstractsNATURAL VARIATION FOR A HYBRID INCOMPATIBILITY BETWEEN TWO SPECIES OF MIMULUSEVOLUTION, Issue 1 2007Andrea L. Sweigart Understanding the process by which hybrid incompatibility alleles become established in natural populations remains a major challenge to evolutionary biology. Previously, we discovered a two-locus Dobzhansky,Muller incompatibility that causes severe hybrid male sterility between two inbred lines of the incompletely isolated wildflower species, Mimulus guttatus and M. nasutus. An interspecific cross between these two inbred lines revealed that the M. guttatus (IM62) allele at hybrid male sterility 1 (hms1) acts dominantly in combination with recessive M. nasutus (SF5) alleles at hybrid male sterility 2 (hms2) to cause nearly complete hybrid male sterility. In this report, we extend these genetic analyses to investigate intraspecific variation for the hms1,hms2 incompatibility in natural populations of M. nasutus and M. guttatus, performing a series of interspecific crosses between individuals collected from a variety of geographic locales. Our results suggest that hms2 incompatibility alleles are common and geographically widespread within M. nasutus, but absent or rare in M. guttatus. In contrast, the hms1 locus is polymorphic within M. guttatus and the incompatibility allele appears to be extremely geographically restricted. We found evidence for the presence of the hms1 incompatibility allele in only two M. guttatus populations that exist within a few kilometers of each other. The restricted distribution of the hms1 incompatibility allele might currently limit the potential for the hms1,hms2 incompatibility to act as a species barrier between sympatric populations of M. guttatus and M. nasutus. Extensive sampling within a single M. guttatus population revealed that the hms1 locus is polymorphic and that the incompatibility allele appears to segregate at intermediate frequency, a pattern that is consistent with either genetic drift or natural selection. [source] The paternal-sex-ratio (PSR) chromosome in natural populations of Nasonia (Hymenoptera: Chalcidoidea)JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 6 2000L. W. Beukeboom Selfish genetic elements may be important in promoting evolutionary change. Paternal sex ratio (PSR) is a selfish B chromosome that causes all-male families in the haplodiploid parasitic wasp Nasonia vitripennis, by inducing paternal genome loss in fertilized eggs. The natural distribution and frequency of this chromosome in North American populations of N. vitripennis was investigated using a combination of phenotypic and molecular assays. Sampling throughout North America failed to recover PSR except from populations in the Great Basin area of western North America. Extensive sampling of Great Basin populations revealed PSR in frequencies ranging from 0 to 6% at different collection sites, and extended its distribution to Idaho and Wyoming. Intensive sampling in upstate New York did not detect the chromosome. Frequencies of the maternal-sex ratio distorter (MSR), son killer (SK) and virgin females ranged from 0 to 12%. Paternal sex ratio may be restricted to the Great Basin because its spread is hampered by geographical barriers, or because populations in other areas are not conducive to PSR maintenance. However, it cannot be ruled out that PSR occurs in other regions at very low frequencies. The apparent limited distribution and low frequency of PSR suggest that it will have relatively little impact on genome evolution in Nasonia. [source] Validating the use of temperature data loggers to measure survival of songbird nestsJOURNAL OF FIELD ORNITHOLOGY, Issue 4 2006Karel Weidinger ABSTRACT Accurate determination of nest fates and nest predators is possible through continuous video monitoring, but such monitoring is relatively expensive and labor intensive. If documenting of the timing of nest termination events is sufficient, then data loggers (DL) may allow more extensive sampling and may represent a viable alternative. I validated temperature DL records of nest survival time by simultaneous videotaping and compared results derived from DL records with those obtained by regular nest visits by an observer. I estimated the fate of 937 nests of nine species of open cup-nesting songbirds, including 673 nests monitored using DL, 165 monitored using video cameras, 33 validation nests monitored simultaneously using both DL and video cameras, and 132 control nests monitored only by observer visits. Deployment of DL did not negatively influence nest survival rate. DL reliably recorded survival time and allowed classification of nest fates based on the potential fledging age, regardless of the frequency of nest visits by an observer. The true fate of nests that survived beyond the potential fledging age can not be safely determined from time of failure, except for nocturnal events that suggest partial predation. Video revealed frequent partial or complete predation on nests with old nestlings that would have been categorized as successful by other methods. I conclude that temperature DL are efficient, reliable, and relatively inexpensive tools for recording exact nest survival times and classification of nest fates, with implications for nest survival modeling and discriminating between diurnal and nocturnal predation. SINOPSIS Es posible determinar con precisión la sobrevicencia en nidos y la depredación en estos mediante el uso de videos contínuos. Pero dicho monitoreo es relativamente costoso y requiere mucho trabajo. Si el documentar el momento en que se termina el anidamiento es suficiente para obtener la información, previamente mencionada, el uso de bitácoras electrónicas de temperatura (loggers) pudieran permitir el tomar muestras más amplias y por ende, representar una alternativa viable. Validé la toma de temperaturas con bitácoras electrónicas para determinar la sobrevivencia en nidos con la toma simultánea de videos y comparé los resultados obtenidos (con la bitácora) con los datos tomados por un observador que visitó regularmente los nidos. El estudio se hizo con 937 nidos de nueve especies de aves canoras cuyo nido es en forma de copa. De estos 673 se monitorearon utilizando bitácoras electrónicas de temperatura, 165 con cámaras de video, 33 con monitoreo simultáneo de bitacora y video y 132, como control, monitoreados mediante observación directa. El uso de las bitácoras no influyó negativamente en la tasa de sobrevivencia. La bitácora grabó el tiempo de sobrervivencia y permitió la clasificación de los nidos (exitoso o no exitoso) basado en el tiempo potencial de la edad de dejar el nido, sin importar la frecuencia de visita a los nidos por parte de observadores. La verdadera finalidad de los nidos que sobreviven, más alla de la edad potencial de dejar el nido los pichones, no puede ser determinado con exactitud, excepto en eventos nocturnos que surgieren depredación. El uso de videos permitió determinar la depredación parcial o completa en nidos, particularmente de pichones que se tardaron más que el tiempo promedio en dejar el nido y que en estudios se asume que sobrevivieron. Puedo concluir que las bitácoras electrónicas de temperatura son eficientes, confiables, de bajo costo y permiten determinar con precisión la sobrevivencia en nidos y la clasificación de estos entre exitosos y no exitosos, con implicaciones para construir modelos de sobrevivencia y discriminar entre depredores diurnos y nocturnos. [source] Genomic islands of speciation or genomic islands and speciation?MOLECULAR ECOLOGY, Issue 5 2010THOMAS L. TURNER Populations of the malaria mosquito, Anopheles gambiae, are comprised of at least two reproductively isolated, sympatric populations. In this issue, White et al. (2010) use extensive sampling, high-density tiling microarrays, and an updated reference genome to clarify and expand our knowledge of genomic differentiation between these populations. It is now clear that DNA near the centromeres of all three chromosomes are in near-perfect disequilibrium with each other. This is in stark contrast to the remaining 97% of the assembled genome, where fixed differences between populations have not been found, and many polymorphisms are shared. This pattern, coupled with direct evidence of hybridization in nature, supports models of "mosaic" speciation, where ongoing hybridization homogenizes variation in most of the genome while loci under strong selection remain in disequilibrium with each other. However, unambiguously demonstrating that selection maintains the association of these pericentric "speciation islands" in the face of gene flow is difficult. Low recombination at all three loci complicates the issue, and increases the probability that selection unrelated to the speciation process alters patterns of variation in these loci. Here, we discuss these different scenarios in light of this new data. [source] Contrasting patterns in genetic diversity following multiple invasions of fresh and brackish watersMOLECULAR ECOLOGY, Issue 12 2006DAVID W. KELLY Abstract Biological invasions may combine the genetic effects of population bottlenecks and selection and thus provide valuable insight into the role of such processes during novel environmental colonizations. However, these processes are also influenced by multiple invasions, the number of individuals introduced and the degree of similarity between source and receiving habitats. The amphipod Gammarus tigrinus provides a useful model to assess these factors, as its invasion history has involved major environmental transitions. This species is native to the northwest Atlantic Ocean, although it invaded both brackish and freshwater habitats in the British Isles after introduction more than 65 years ago. It has also spread to similar habitats in Western Europe and, most recently, to Eastern Europe, the Baltic Sea, and the Laurentian Great Lakes. To examine sources of invasion and patterns of genetic change, we sampled populations from 13 native estuaries and 19 invaded sites and sequenced 542 bp of the mitochondrial COI gene. Strong native phylogeographical structure allowed us to unambiguously identify three allopatrically evolved clades (2.3,3.1% divergent) in invading populations, indicative of multiple introductions. The most divergent clades occurred in the British Isles and mainland Europe and were sourced from the St Lawrence and Chesapeake/Delaware Bay estuaries. A third clade was found in the Great Lakes and sourced to the Hudson River estuary. Despite extensive sampling, G. tigrinus did not occur in freshwater at putative source sites. Some European populations showed reduced genetic diversity consistent with bottlenecks, although selection effects cannot be excluded. The habitat distribution of clades in Europe was congruent with the known invasion history of secondary spread from the British Isles. Differences in salinity tolerance among lineages were suggested by patterns of habitat colonization by different native COI clades. Populations consisting of admixtures of the two invading clades were found principally at recently invaded fresh and brackish water sites in Eastern Europe, and were characterized by higher genetic diversity than putative source populations. Further studies are required to determine if these represent novel genotypes. Our results confirm that biological invasions need not result in diminished genetic diversity, particularly if multiple source populations, each with distinctive genetic composition, contribute to the founding populations. [source] Extensive Sampling Changes T-Staging of Infiltrating Lobular Carcinoma of Breast: A Comparative Study of Gross versus Microscopic Tumor SizesTHE BREAST JOURNAL, Issue 6 2006Neda A. Moatamed MD Abstract:, Infiltrating lobular carcinoma represents 7,10% of all invasive breast cancers. The greatest diameter of the tumors in the surgical specimens is required for an accurate T-staging. Tumors with dimension of zero cm, >0 to ,2 cm, >2 to ,5 cm, and >5 cm are staged as T0, T1, T2, and T3, respectively. A retrospective study on the specimens was performed on the specimens of 74 cases with infiltrating lobular carcinoma at the UCLA Medical Center from 2003 to 2005. The patients' ages ranged from 38 to 95 years. Specimens were from lumpectomy and mastectomy procedures on 36 and 38 patients, respectively. The specimens were divided in four groups according to the gross T-stages. Microscopic measurement of the tumors was carried out within each of the four groups for restaging purposes. Resizing of tumors was performed by marking the microscopic tumor extensions and compiling the measurements. In group 1, all 26 gross T0 tumors changed to T1 (69%), T2 (19%), and T3 (12%) after microscopic restaging. In group 2, 50% of the 26 gross T1 tumors became T2 (35%) and T3 (15%). In group 3, 9 (50%) of the T2 tumors changed to T3 microscopically. All 7 specimens (100%) in group 4 remained as T3. The results show that the gross measurements alone may underestimate 40,50% of the tumor T-stages. Therefore, the T-stages of the tumors with a gross size of 5 cm or less may change by microscopic resizing after an extensive sampling of the specimen. [source] Bayesian Prediction of Spatial Count Data Using Generalized Linear Mixed ModelsBIOMETRICS, Issue 2 2002Ole F. Christensen Summary. Spatial weed count data are modeled and predicted using a generalized linear mixed model combined with a Bayesian approach and Markov chain Monte Carlo. Informative priors for a data set with sparse sampling are elicited using a previously collected data set with extensive sampling. Furthermore, we demonstrate that so-called Langevin-Hastings updates are useful for efficient simulation of the posterior distributions, and we discuss computational issues concerning prediction. 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