Journal articles on the topic 'Among-site rate variation'
To see the other types of publications on this topic, follow the link: Among-site rate variation.
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 journal articles for your research on the topic 'Among-site rate variation.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.
1
Sullivan, Jack. "Combining Data with Different Distributions of Among-Site Rate Variation." Systematic Biology 45, no. 3 (September 1, 1996): 375–80. http://dx.doi.org/10.1093/sysbio/45.3.375.
Full text
2
Yang, Ziheng. "Among-site rate variation and its impact on phylogenetic analyses." Trends in Ecology & Evolution 11, no. 9 (September 1996): 367–72. http://dx.doi.org/10.1016/0169-5347(96)10041-0.
Full text
3
Sullivan, Jack, Kent E. Holsinger, and Chris Simon. "The effect of topology on estimates of among-site rate variation." Journal of Molecular Evolution 42, no. 2 (February 1996): 308–12. http://dx.doi.org/10.1007/bf02198857.
Full text
4
Zhang, Jianzhi, and Xun Gu. "Correlation Between the Substitution Rate and Rate Variation Among Sites in Protein Evolution." Genetics 149, no. 3 (July 1, 1998): 1615–25. http://dx.doi.org/10.1093/genetics/149.3.1615.
Full textAbstract:
Abstract It is well known that the rate of amino acid substitution varies among different proteins and among different sites of a protein. It is, however, unclear whether the extent of rate variation among sites of a protein and the mean substitution rate of the protein are correlated. We used two approaches to analyze orthologous protein sequences of 51 nuclear genes of vertebrates and 13 mitochondrial genes of mammals. In the first approach, no assumptions of the distribution of the rate variation among sites were made, and in the second approach, the gamma distribution was assumed. Through both approaches, we found a negative correlation between the extent of among-site rate variation and the average substitution rate of a protein. That is, slowly evolving proteins tend to have a high level of rate variation among sites, and vice versa. We found this observation consistent with a simple model of the neutral theory where most sites are either invariable or neutral. We conclude that the correlation is a general feature of protein evolution and discuss its implications in statistical tests of positive Darwinian selection and molecular time estimation of deep divergences.
5
Tajima, Fumio. "The Amount of DNA Polymorphism Maintained in a Finite Population When the Neutral Mutation Rate Varies Among Sites." Genetics 143, no. 3 (July 1, 1996): 1457–65. http://dx.doi.org/10.1093/genetics/143.3.1457.
Full textAbstract:
Abstract The expectations of the average number of nucleotide differences per site (π), the proportion of segregating site (s), the minimum number of mutations per site (s*) and some other quantities were derived under the finite site models with and without rate variation among sites, where the finite site models include Jukes and Cantor's model, the equal-input model and Kimura's model. As a model of rate variation, the gamma distribution was used. The results indicate that if distribution parameter α is small, the effect of rate variation on these quantities are substantial, so that the estimates of θ based on the infinite site model are substantially underestimated, where θ = 4Nv, N is the effective population size and vis the mutation rate per site per generation. New methods for estimating θ are also presented, which are based on the finite site models with and without rate variation. Using these methods, underestimation can be corrected.
6
Van de Peer, Yves, and Rupert De Wachter. "Evolutionary Relationships Among the Eukaryotic Crown Taxa Taking into Account Site-to-Site Rate Variation in 18S rRNA." Journal of Molecular Evolution 45, no. 6 (December 1997): 619–30. http://dx.doi.org/10.1007/pl00006266.
Full text
7
Reyes, Aurelio, Graziano Pesole, and Cecilia Saccone. "Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny." Gene 259, no. 1-2 (December 2000): 177–87. http://dx.doi.org/10.1016/s0378-1119(00)00438-8.
Full text
8
Sheffield, Nathan C. "The Interaction between Base Compositional Heterogeneity and Among-Site Rate Variation in Models of Molecular Evolution." ISRN Evolutionary Biology 2013 (December 26, 2013): 1–8. http://dx.doi.org/10.5402/2013/391561.
Full textAbstract:
Many commonly used models of molecular evolution assume homogeneous nucleotide frequencies. A deviation from this assumption has been shown to cause problems for phylogenetic inference. However, some claim that only extreme heterogeneity affects phylogenetic accuracy and suggest that violations of other model assumptions, such as variable rates among sites, are more problematic. In order to explore the interaction between compositional heterogeneity and variable rates among sites, I reanalyzed 3 real heterogeneous datasets using several models. My Bayesian inference recovers accurate topologies under variable rates-among-sites models, but fails under some models that account for compositional heterogeneity. I also ran simulations and found that accounting for rates among sites improves topology accuracy in compositionally heterogeneous data. This indicates that in some cases, models accounting for among-site rate variation can improve outcomes for data that violates the assumption of compositional homogeneity.
9
Meyer, Austin G., Eric T. Dawson, and Claus O. Wilke. "Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1614 (March 19, 2013): 20120334. http://dx.doi.org/10.1098/rstb.2012.0334.
Full textAbstract:
We investigate the causes of site-specific evolutionary-rate variation in influenza haemagglutinin (HA) between human and avian influenza, for subtypes H1, H3, and H5. By calculating the evolutionary-rate ratio, ω = d N /d S as a function of a residue's solvent accessibility in the three-dimensional protein structure, we show that solvent accessibility has a significant but relatively modest effect on site-specific rate variation. By comparing rates within HA subtypes among host species, we derive an upper limit to the amount of variation that can be explained by structural constraints of any kind. Protein structure explains only 20–40% of the variation in ω . Finally, by comparing ω at sites near the sialic-acid-binding region to ω at other sites, we show that ω near the sialic-acid-binding region is significantly elevated in both human and avian influenza, with the exception of avian H5. We conclude that protein structure, HA subtype, and host biology all impose distinct selection pressures on sites in influenza HA.
10
Waters, C., G. Melville, and A. Grice. "Genotypic variation among sites within eleven Australian native grasses." Rangeland Journal 25, no. 1 (2003): 70. http://dx.doi.org/10.1071/rj03006.
Full textAbstract:
Eleven species of native grass were collected from 51 sites throughout western New South Wales and south-west Queensland. Approximately 10 whole plants of each species were collected from a site but not all species were collected from each site. Plants were grown in a common environment at Trangie in central western New South Wales and plant morphological and floristic characteristics measured. Data reported here are for observations made in the third year, by which time differences between populations were likely to be more genetic than environmental. Principal component and discriminant analyses revealed a strong relationship between site of origin and plant morphological characteristics, which explained between 61% and 93% of the variation within species. For all but one species, site was significantly correlated with these morphological characteristics. Site could be predicted from morphological characters with a success rate usually greater than 80%. These morphological characteristics must reflect genotypic differences among the collection from the different sites. We were unable to relate this variation to any of a range of site characteristics. Distance between sites could not be used as an indicator of morphological differences between populations. The implications of these findings are discussed in terms of providing strong evidence for the existence of ecotypes and for obtaining appropriate seed sources for revegetation/restoration programs.
11
Handford, Paul. "Trill rate dialects in the Rufous-collared Sparrow, Zonotrichia capensis, in northwestern Argentina." Canadian Journal of Zoology 66, no. 12 (December 1, 1988): 2658–70. http://dx.doi.org/10.1139/z88-391.
Full textAbstract:
Geographical variation in trill rate of Zonotrichia capensis was assessed in a sample of about 2300 individuals from nearly 600 sites distributed throughout northwestern Argentina, from 22 to 34°S. The variation was partitioned among the following site characteristics: original (natural) vegetation, contemporary vegetation structure, latitude, longitude, and altitude. About 45% of the variation was attributable to the original vegetation (p < 0.0001): the other site characteristics explained a further 4%. Thus the geographical distribution of trill rate closely paralleled that of the natural vegetation, even where this vegetation has been long (80–200 years) replaced by various forms of agriculture. These results were interpreted as the consequence of vocal learning influenced by the vocalizations of dominant elements in the local avifauna of each habitat, together with factors affecting the unambiguous propagation of acoustic signals through given kinds of vegetation.
12
SONG, HOJUN, NATHAN C. SHEFFIELD, STEPHEN L. CAMERON, KELLY B. MILLER, and MICHAEL F. WHITING. "When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics." Systematic Entomology 35, no. 3 (March 1, 2010): 429–48. http://dx.doi.org/10.1111/j.1365-3113.2009.00517.x.
Full text
13
Karim, Safiya, Kelly Brennan, Yingwei Peng, William J. Mackillop, and Christopher M. Booth. "Estimating the optimal rate of adjuvant chemotherapy utilization in stage III colon cancer." Journal of Clinical Oncology 35, no. 15_suppl (May 20, 2017): 6591. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.6591.
Full textAbstract:
6591 Background: Identifying optimal chemotherapy utilization rates can drive improvements in quality of care. We report a benchmarking approach to estimate the optimal rate of adjuvant chemotherapy (ACT) for stage III colon cancer. Methods: The Ontario Cancer Registry was linked to electronic chemotherapy records to identify ACT utilization among a random 25% sample of patients with stage III colon cancer diagnosed during 2002-2008 in Ontario, Canada. We explored whether hospital factors (teaching status, regional cancer centre, medical oncologist on-site) were associated with ACT rates. The benchmark population included hospitals with the highest ACT rates that accounted for 10% of the patient population. Hospital ACT rates were adjusted for case mix in a multi-level model accounting for random variation at the hospital level. A Monte Carlo simulation was used to estimate the proportion of observed ACT rate variation that could be due to chance alone. Results: The study population included 2,801patients with stage III colon cancer; ACT was delivered to 66% (1861/2801) of patients. There was no difference in hospital ACT rate by teaching status (64% academic vs 67% non-academic, p = 0.107), comprehensive cancer centre status (65% cancer centre vs 67% non-cancer centre, p = 0.362), or having medical oncology on site (67% on site vs 66% not on site, p = 0.840). After excluding hospitals that had case volumes less than 10 (N = 150), unadjusted ACT rates varied across hospitals (range 44% to 91%, p = 0.017). The unadjusted benchmark ACT rate was 81% (95%CI 76%-86%); utilization rate in non-benchmark hospitals was 65% (95%CI 63%-66%). When using adjusted ACT rates in a multi-level model significant variation remained across hospitals (p < 0.001). The adjusted benchmark ACT rate was 74% (95%CI 63%-83%); non-benchmark hospital ACT rate was 65% (95%CI 53%-75%). The simulation analysis suggested that the non-random component of ACT rate variation across hospitals was 1.5%. Conclusions: There is significant variation in ACT rates across hospitals in routine practice. The estimated benchmark ACT rate is 74%. However, simulation analyses suggest that most of the variation in ACT utilization across hospitals may be due to chance alone.
14
Doebley, J., W. Renfroe, and A. Blanton. "Restriction Site Variation in the Zea Chloroplast Genome." Genetics 117, no. 1 (September 1, 1987): 139–47. http://dx.doi.org/10.1093/genetics/117.1.139.
Full textAbstract:
ABSTRACT Nineteen accessions selected from the four species and three subspecies of the genus Zea and one accession from the related genus Tripsacum were surveyed for variation with 21 restriction endonucleases. In all, 580 restriction sites were assayed in each chloroplast (cp)DNA, this representing 2.2% of the genome. Twenty-four of the 580 sites were variable in one or more of the cpDNAs. The number of nucleotide substitutions per site (p) between Zea and Tripsacum (0.0056) approximates that between other closely related angiosperm genera. The range in values of p among Zea species (0.0003-0.0024) is on the lower end of the range reported for other angiosperm genera. Analysis of the distribution of restriction site mutations throughout the genome indicated that the inverted repeat evolves more slowly than either the small or large unique sequence regions. Parsimony phylogenetic analysis of the restriction site data produced a tree consistent with isoenzymatic and morphological measures of affinity among the species. Chloroplast DNA analysis was not useful in discriminating the subspecies within Zea mays. The lack of any detectable differences between the cpDNA of maize (Z. mays subsp. mays) and some teosintes (Z. mays subsps. mexicana and parviglumis) is consistent with the hypothesis that maize is a domesticated form of teosinte. Comparison of the degree of sequence divergence for Z. mays cpDNA and the Adh1 locus suggests the latter may be evolving at 10 times the rate of the former. Comparison of rates of sequence evolution for the mitochondrial and chloroplast genomes was inconclusive and could not clarify whether these two genomes have dissimilar rates of sequence evolution.
15
Chen, Zhong, Thomas E. Kolb, Karen M. Clancy, Valerie D. Hipkins, and Laura E. DeWald. "Allozyme variation in interior Douglas-fir: association with growth and resistance to western spruce budworm herbivory." Canadian Journal of Forest Research 31, no. 10 (October 1, 2001): 1691–700. http://dx.doi.org/10.1139/x01-107.
Full textAbstract:
We used starch gel electrophoresis to investigate levels of genetic variation between trees of interior Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. glauca) that were phenotypically resistant versus susceptible to defoliation by the western spruce budworm (Choristoneura occidentalis Freeman). We also investigated the association between allozyme variation and tree growth traits. Overall, the phenotypically resistant trees had a lower allelic heterozygosity (p = 0.020) compared with susceptible trees. However, this difference between resistant and susceptible trees primarily occurred at the Buena Vista, Colorado, site rather than the Deckers, Colorado, and Jacob Lake, Arizona, sites. Among 25 loci we examined, the resistant trees also had a higher frequency of the most common alleles (p = 0.057) and a higher proportion of homozygous genotypes, especially at loci FEST-1 (p = 0.004), ACO-1 (p = 0.080), and 6PGD-1 (p = 0.084). The higher allelic heterozygosity in susceptible trees was mainly due to their higher proportion of uncommon and (or) rare alleles. Compared with susceptible trees, resistant trees had higher mean radial growth rates (p = 0.047) and less temporal variability in growth rate over 25 years (p = 0.037). Mean radial growth rate and average tree heterozygosity were not related at any site (p = 0.316). Relationships between temporal variability in growth rate and tree heterozygosity were inconsistent among sites. Our results suggest that phenotypic differences in resistance of interior Douglas-fir to western spruce budworm defoliation are partly caused by genetic differences among trees.
16
Zhou, Jizhong, Andrzej Kilian, Robert L. Warner, and Andris Kleinhofs. "Variation of nitrate reductase genes in selected grass species." Genome 38, no. 5 (October 1, 1995): 919–27. http://dx.doi.org/10.1139/g95-121.
Full textAbstract:
In order to study the variation of nitrate reductase (NR) genes among grass species, gene number, intron size and number, and the heme-hinge fragment sequence of 25 grass species were compared. Genomic DNA cut with six restriction enzymes and hybridized with the barley NAD(P)H and NADH NR gene probes revealed a single NAD(P)H NR gene copy and two or more NADH NR gene copies per haploid genome in most of the species examined. Major exceptions were Hordeum vulgare, H. vulgare ssp. spontaneum, and Avena strigosa, which appeared to have a single NADH NR gene copy. The NADH NR gene intron number and lengths were examined by polymerase chain reaction amplification. Introns I and III appeared to be absent in at least one of the NADH NR genes in the grass species, while intron II varied from 0.8 to 2.4 kilobases in length. The NADH NR gene heme-hinge regions were amplified and sequenced. The estimated average overall nucleotide substitution rate in the sequenced region was 7.8 × 10−10 substitutions/site per year. The synonymous substitution rate was 2.11 × 10−9 substitutions/synonymous site per year and the nonsynonymous substitution rate was 4.10 × 10−10 substitutions/nonsynonymous site per year. Phylogenetic analyses showed that all of the wild Hordeum species examined clustered in a group separate from H. vulgare and H. vulgare ssp. spontaneum.Key words: nitrate reductase gene, gene copy number, intron, molecular phylogeny, grasses.
17
Hoenen, T., D. Safronetz, A. Groseth, K. R. Wollenberg, O. A. Koita, B. Diarra, I. S. Fall, et al. "Mutation rate and genotype variation of Ebola virus from Mali case sequences." Science 348, no. 6230 (March 26, 2015): 117–19. http://dx.doi.org/10.1126/science.aaa5646.
Full textAbstract:
The occurrence of Ebola virus (EBOV) in West Africa during 2013–2015 is unprecedented. Early reports suggested that in this outbreak EBOV is mutating twice as fast as previously observed, which indicates the potential for changes in transmissibility and virulence and could render current molecular diagnostics and countermeasures ineffective. We have determined additional full-length sequences from two clusters of imported EBOV infections into Mali, and we show that the nucleotide substitution rate (1.3 × 10–3 substitutions per site per year) is consistent with rates observed in Central African outbreaks. In addition, overall variation among all genotypes observed remains low. Thus, our data indicate that EBOV is not undergoing rapid evolution in humans during the current outbreak. This finding has important implications for outbreak response and public health decisions and should alleviate several previously raised concerns.
18
Manning, G., L. G. Fuller, R. G. Eilers, and I. Florinsky. "Soil moisture and nutrient variation within an undulating Manitoba landscape." Canadian Journal of Soil Science 81, no. 4 (August 1, 2001): 449–58. http://dx.doi.org/10.4141/s00-058.
Full textAbstract:
The use of discrete management units for variable-rate N fertilization requires that factors influencing grain yield response to N fertilizer are adequately characterized by delineating landscapes into such management units. The objective of this study was to compare the use of topographically derived landform element complexes (LEC) and the use of individual soil series as management units. Soil volumetric moisture content, nitrate-N, exchangeable ammonium-N, extractable phosphorus, exchangeable potassium, and sulphate-sulphur were studied in 10 intensively sampled transects in an undulating glacial till landscape near Miniota, Manitoba. The study site was delineated into upper, mid and lower LEC using a digital elevation model derived from relative elevation data. The LEC were useful in capturing gross variability at a manageable landscape scale. Among LEC there was a general trend of lower > mid > upper for median values of soil moisture, nitrate, phosphate, potassium and sulphate, as these attributes generally increased with convergent landscape character. Differences among LEC were often statistically significant, and relative distributions exhibited temporal persistence. The site was also stratified by soil series, including Newdale, Varcoe and Angusville soils (Black Chernozems), which were identified by examination of individual soil cores at each sample point. Stratifying the site into management units using soil genetic information, which is reflective of historical moisture conditions and biomass production, was expected to be superior. There was little advantage, however, in using soil series rather than LEC. Spatial distributions of the most agronomically relevant attributes (soil moisture and nitrate) were expressed at a landscape scale broader than that at which soil series occurred within the site. While there were important differences among soil series with respect to nutrients such as phosphate and sulphate, the site was better stratified by LEC with respect to soil moisture and nitrate. Key words: Soil-landscape, soil series, soil moisture, soil residual nitrate, extractable phosphorus
19
Taylor, Jolyn S., Claire A. Marten, Kimberly A. Potts, Lynn M. Cloutier, Katherine E. Cain, Shauna L. Fenton, Tara N. Tatum, et al. "What Is the Real Rate of Surgical Site Infection?" Journal of Oncology Practice 12, no. 10 (October 2016): e878-e883. http://dx.doi.org/10.1200/jop.2016.011759.
Full textAbstract:
Purpose: Surgical site infections (SSIs) are associated with patient morbidity and increased health care costs. Although several national organizations including the University HealthSystem Consortium (UHC), the National Surgical Quality Improvement Program (NSQIP), and the National Healthcare Safety Network (NHSN) monitor SSI, there is no standard reporting methodology. Methods: We queried the UHC, NSQIP, and NHSN databases from July 2012 to June 2014 for SSI after gynecologic surgery at our institution. Each organization uses different definitions and inclusion and exclusion criteria for SSI. The rate of SSI was also obtained from chart review from April 1 to June 30, 2014. SSI was classified as superficial, deep, or organ space infection. The rates reported by the agencies were compared with the rates obtained by chart review using Fisher’s exact test. Results: Overall SSI rates for the databases were as follows: UHC, 1.5%; NSQIP, 8.8%; and NHSN, 2.8% (P < .001). The individual databases had wide variation in the rate of deep infection (UHC, 0.7%; NSQIP, 4.7%; NHSN, 1.3%; P < .001) and organ space infection (UHC, 0.4%; NSQIP, 4.4%; NHSN, 1.4%; P < .001). In agreement with the variation in reporting methodology, only 19 cases (24.4%) were included in more than one database and only one case was included in all three databases (1.3%). Conclusion: There is discordance among national reporting agencies tracking SSI. Adopting standardized metrics across agencies could improve consistency and accuracy in assessing SSI rates.
20
Sharma, Sandeep. "Prevalence and Epidemiological Variation of Oral Squamous Cell Carcinoma among Population of Central Nepal." Journal of College of Medical Sciences-Nepal 15, no. 4 (December 31, 2019): 267–69. http://dx.doi.org/10.3126/jcmsn.v15i4.24109.
Full textAbstract:
Background: Squamous cell carcinoma (SCC) is the most common malignant neoplasm of the oral cavity and represents about 90% of all oral malignancies. Oral squamous cell carcinoma (OSCC) is an important cause of morbidity and mortality worldwide with an incidence rate that varies widely by geographic location. The purpose of this study was to identify any trends in prevalence at specific anatomic sites or within specific age or sex groups of OSCCs in Chitwan population of Nepal.
Methods: The study covers the period between January 2016 and October 2018. OSCC cases were retrospectively analysed for site, age, gender and habits and the findings were formulated to chart the trends in Chitwan population.
Results: The study revealed a male to female ratio of 2.45:1 with the largest number of OSCCs developing in the fourth and fifth decades of life. Most commonly affected site was the buccal mucosa (66.06%), followed by retromolar area (19%), floor of the mouth (10.41%), lateral border of the tongue (1.81%), labial mucosa (2.26%), and palate (0.45%). Smokeless tobacco habit was more prevalent than smoking tobacco in both men as well as women. Chi Square test was done to show association between different variables i.e. between gender to site and gender to habit and gender to different grades of cancer, which were found to be non-significant.
Conclusions: Oral cancer is an important cause of morbidity and mortality worldwide with an incidence rate that varies widely by geographic location. Even within one geographical location, the variations are seen among groups categorized by age, sex, site or habit.
21
Leon, Ramon G., and Barry L. Tillman. "Postemergence Herbicide Tolerance Variation in Peanut Germplasm." Weed Science 63, no. 2 (June 2015): 546–54. http://dx.doi.org/10.1614/ws-d-14-00128.1.
Full textAbstract:
Although herbicide tolerance is not usually evaluated until the final stages of breeding programs, this trait is very important for grower adoption of new peanut cultivars. Understanding herbicide tolerance of breeding lines could help breeders develop selection strategies that maximize herbicide tolerance in new commercial cultivars. However, little is known about herbicide tolerance variability in peanut germplasm. Thirty-five randomly selected breeding lines from the peanut mini-core collection and cultivars ‘Florida-07’ and ‘Georgia-06G’ were evaluated for tolerance to 11 herbicides under greenhouse conditions. Variation among peanut lines in herbicide tolerance, measured as dry weight reductions (DWR), was similar across herbicides and was normally distributed. Florida-07 and Georgia-06G were in the lower two quartiles of injury and DWR among the evaluated peanut lines. Dose–response experiments showed that the most tolerant breeding lines had I50(the rate required to cause 50% injury) and GR50(the rate required to reduce dry weight 50%) values 0.4 to 2.5 times higher than the most susceptible lines, depending on the herbicide. A breeding line had a dicamba GR5013 times higher than the most susceptible line and 2.8 and 4.7 times higher than Florida-07 and Georgia-06G, respectively. The most tolerant lines were consistently tolerant to herbicides with different mechanisms of action, suggesting that nontarget site mechanisms are more likely to be responsible for the tolerance than target-site mutations. These results confirmed peanut-breeding programs would greatly benefit from screening breeding lines for tolerance to key herbicides and developing an herbicide-tolerance catalog. This information can be used when designing new crosses to reduce the risk of developing cultivars with low herbicide tolerance especially considering that one-half of the breeding lines exhibited lower tolerance than the commercial cultivars.
22
Lynch, M., and P. E. Jarrell. "A method for calibrating molecular clocks and its application to animal mitochondrial DNA." Genetics 135, no. 4 (December 1, 1993): 1197–208. http://dx.doi.org/10.1093/genetics/135.4.1197.
Full textAbstract:
Abstract A generalized least-squares procedure is introduced for the calibration of molecular clocks and applied to the complete mitochondrial DNA sequences of 13 animal species. The proposed technique accounts for both nonindependence and heteroscedasticity of molecular-distance data, problems that have not been taken into to account in such analyses in the past. When sequence-identity data are transformed to account for multiple substitutions/site, the molecular divergence scales linearly with time, but with substantially more variation in the substitution rate than expected under a Poisson model. Significant levels of divergence are predicted at zero divergence time for most loci, suggesting high levels of site-specific heterozygosity among mtDNA molecules establishing in sister taxa. For nearly all loci, the baseline heterozygosity is lower and the substitution rate is higher in mammals relative to other animals. There is considerable variation in the evolutionary rate among loci but no compelling evidence that the average rate of mtDNA evolution is elevated with respect to that of nuclear DNA. Using the observed patterns of interspecific divergence, empirical estimates are derived for the mean coalescence times of organelles colonizing sister taxa.
23
Burton, Andrew J., Kurt S. Pregitzer, Gregory P. Zogg, and Donald R. Zak. "Latitudinal variation in sugar maple fine root respiration." Canadian Journal of Forest Research 26, no. 10 (October 1, 1996): 1761–68. http://dx.doi.org/10.1139/x26-200.
Full textAbstract:
A changing global climate may impact the respiration of fine roots. While many models adjust fine root respiration as temperature increases, the influence of soil nutrient availability and the possibility that root respiration may be adapted to local climate are often not addressed. Rates of fine root respiration were measured in four sugar maple (Acersaccharum Marsh.) forests located along a latitudinal gradient in Michigan. Root respiration was measured as O2 consumption at temperatures ranging from 6 to 24 °C on excised fine root samples in early September, October, and November of 1994. Root respiration increased exponentially with temperature with an average Q10 of 2.7; there were no differences in Q10 among sites. However, there were differences among sites in mean respiration rate at a given temperature. This site effect did not indicate ecotypic adaptation to local climate, but rather reflected fine root N concentration. Respiration at a given temperature was consistently higher in roots with higher N concentrations, and higher root N concentrations always occurred at sites having greater N mineralization rates. Results suggest increases in soil temperature could significantly alter root respiration C flux at these sites, as could changes in site N availability associated with chronic N deposition or altered N mineralization resulting from global climate change.
24
Sanz, Juan José. "Latitudinal Variation in Female Local Return Rate in the Philopatric Pied Flycatcher (Ficedula hypoleuca)." Auk 118, no. 2 (April 1, 2001): 539–43. http://dx.doi.org/10.1093/auk/118.2.539.
Full textAbstract:
Abstract Philopatry and dispersal distances of female Pied Flycatcher (Ficedula hypoleuca) are presented for European populations using data from 25 breeding areas from 40 to 70°N. Female annual survival probabilities according to capture–recapture models were similar in two study areas in central Spain (45 and 52%). The present study shows that survival is underestimated by using annual local return rate in one of the two breeding populations under study in central Spain. In southern and central Europe, females were found to return equally regularly to their breeding areas, whereas in northern Europe (latitude >60°N) females returned at lower rates. I did not find that median dispersal distance varied among sites, nor was breeding distance related to locate survival rate. Therefore, the present study suggests that the decline in between-year local return rate of female Pied Flycatchers with increasing latitude over Europe may be more probably caused by differences in mortality than by geographical differences in site fidelity.
25
Liu, Wenwen, Gregory E. MacDonald, J. Bryan Unruh, Kevin E. Kenworthy, Laurie E. Trenholm, and Ramon G. Leon. "Variation in tolerance mechanisms to fluazifop-P-butyl among selected zoysiagrass lines." Weed Science 67, no. 3 (April 5, 2019): 288–95. http://dx.doi.org/10.1017/wsc.2019.6.
Full textAbstract:
AbstractBreeding herbicide tolerance into new cultivars can improve safety and weed control in turfgrass systems. The sensitivity to fluazifop-P-butyl of 27 zoysiagrass (Zoysiaspp.) lines was screened under greenhouse conditions to identify potential tolerant germplasm for breeding programs. The herbicide rate that caused 50% biomass reduction (GR50) and the rate that caused 50% injury (ID50) were calculated to select the three most-tolerant and the five most-susceptible lines for studying the physiological mechanisms responsible for fluazifop-P-butyl tolerance. The differences in GR50and ID50between susceptible and tolerant lines ranged from 4-fold to more than 10-fold. Cytochrome P450–mediated metabolism was not detected in fluazifop-P-butyl–tolerant lines. Sequencing of theACCasegene confirmed that none of the seven previously reported mutations conferring resistance to acetyl-CoA carboxylase (ACCase)-inhibiting herbicides in other species were present in any of the tolerant or susceptible zoysiagrass lines studied. An Ala-2073-Thr substitution was identified in two tolerant lines, but this mutation did not completely explain the tolerant phenotype. No clear differences in absorption and translocation rates of14C-radiolabeled fluazifop-P-butyl were observed among most lines, with the exception of a susceptible line that exhibited greater translocation than two of the tolerant lines. Metabolite profiles did not differ between tolerant and susceptible lines. Our results suggest that the diversity in tolerance to fluazifop-P-butyl in zoysiagrass germplasm is most likely the result of a combination of different, minor, additive non–target site mechanisms such as translocation rate and compartmentation after absorption.
26
Mills, William R., Janet M. Buccola, Jamie Roosa, Lisa Lemin, Lynn Cappelli, and Belinda Schraer. "Variation in Value-Based Outcome Measures Among Assisted Living Communities Served by a Home-Based Primary Care Practice During COVID-19." Home Health Care Management & Practice 33, no. 1 (October 5, 2020): 45–48. http://dx.doi.org/10.1177/1084822320963094.
Full textAbstract:
We aimed to determine the hospitalization rate and average days spent at home in a population of assisted living (AL) residents served by a home-based primary care (HBPC) practice during the COVID-19 pandemic. We provided on-site HBPC to 1,699 AL residents and calculated hospitalization rate and days spent at home. The AL population had a mean age of 84 ± 10 years and 73% were female. The mean hospitalization rate was 449 admissions per 1,000 per year, and there was wide variation among AL communities. AL residents spent a mean of 358 days at home per year, and the average days spent at home varied during the COVID-19 pandemic. Use of these measures may help AL articulate its value proposition by enabling seniors with complex health needs to live in community settings for as many days as possible.
27
L'Abée-Lund, Jan Henning. "Variation within and between Rivers in Adult Size and Sea Age at Maturity of Anadromous Brown Trout, Salmo trutta." Canadian Journal of Fisheries and Aquatic Sciences 48, no. 6 (June 1, 1991): 1015–21. http://dx.doi.org/10.1139/f91-119.
Full textAbstract:
I compared adult size and sea age at sexual maturity among nine populations of anadromous brown trout, Salmo trutta, in two Norwegian rivers to determine the extent of inter- and intrariverine variations. Variation in the mean length of spawners and in the mean sea age at sexual maturity were mainly dependent on the variations found within rather than between rivers. Mean lengths and mean age at maturity of males increased significantly with increasing altitude of the spawning area and with migration distance in freshwater. In females, positive significant correlations were found with mean lengths and altitude of the spawning area and with mean sea age at maturity and both spawning site altitude and migration distance. Mean lengths and ages of males and females were not significantly correlated with the rate of water discharge in the streams during spawning. The size of gravel substrate for spawning was of minor importance in explaining interpopulation variation in mean female size. The increase noted in mean length and in mean sea age at maturity of both males and females is probably an adaptation to greater energy expenditure to reach the uppermost natal spawning areas.
28
Klaoudatos, Dimitris, Zoi Kotsiri, Nikos Neofitou, Alexios Lolas, and Dimitris Vafidis. "Population Characteristics of the Mid-Littoral Chthamalid Barnacle C. stellatus (Poli, 1791) in Eastern Mediterranean (Central Greece)." Water 12, no. 12 (November 24, 2020): 3304. http://dx.doi.org/10.3390/w12123304.
Full textAbstract:
Barnacles are key space-occupiers in rocky shore communities on European coasts. Barnacles of the species Chthamalus stellatus (Poli, 1791) were collected between June 2014 and May 2015 from two sites, two stations per each site with varying degree of exposure to wave action and anthropogenic pressure (trampling), in the Eastern Mediterranean (Pagasitikos Gulf, Central Greece). This study addresses a knowledge gap in population characteristics of C. stellatus populations in the Eastern Mediterranean, assessing population structure and allometric relationships. Patterns of distribution and abundance (density and percentage cover) were studied both temporally (seasonally) and spatially (water level and site). Morphometric characteristics exhibited spatiotemporal variation. Population density was significantly higher at the site with higher wave exposure. The population cover exhibited high levels of similarity among shore levels, both spatially and temporally. Spatial distribution exhibited a clumped pattern of dispersion in autumn, winter, and spring, mainly in the sheltered site. Six dominant age groups were identified, with the dominant cohort in the third-year class. Significant negative allometric relationships were exhibited between all morphometric characteristics. Differences in growth patterns among populations were indicated, with a higher rate of growth at the site of lower wave exposure.
29
Ho, Eddie K. H., Emily S. Bellis, Jaclyn Calkins, Jeffrey R. Adrion, Leigh C. Latta IV, and Sarah Schaack. "Engines of change: Transposable element mutation rates are high and variable within Daphnia magna." PLOS Genetics 17, no. 11 (November 1, 2021): e1009827. http://dx.doi.org/10.1371/journal.pgen.1009827.
Full textAbstract:
Transposable elements (TEs) represent a major portion of most eukaryotic genomes, yet little is known about their mutation rates or how their activity is shaped by other evolutionary forces. Here, we compare short- and long-term patterns of genome-wide mutation accumulation (MA) of TEs among 9 genotypes from three populations of Daphnia magna from across a latitudinal gradient. While the overall proportion of the genome comprised of TEs is highly similar among genotypes from Finland, Germany, and Israel, populations are distinguishable based on patterns of insertion site polymorphism. Our direct rate estimates indicate TE movement is highly variable (net rates ranging from -11.98 to 12.79 x 10−5 per copy per generation among genotypes), differing both among populations and TE families. Although gains outnumber losses when selection is minimized, both types of events appear to be highly deleterious based on their low frequency in control lines where propagation is not limited to random, single-progeny descent. With rate estimates 4 orders of magnitude higher than base substitutions, TEs clearly represent a highly mutagenic force in the genome. Quantifying patterns of intra- and interspecific variation in TE mobility with and without selection provides insight into a powerful mechanism generating genetic variation in the genome.
30
CUMMING, GRAEME S., ERIC SHEPARD, SHARON OKANGA, ALEXANDRE CARON, MDUDUZI NDLOVU, and JEFFREY L. PETERS. "Host associations, biogeography, and phylogenetics of avian malaria in southern African waterfowl." Parasitology 140, no. 2 (October 12, 2012): 193–201. http://dx.doi.org/10.1017/s0031182012001461.
Full textAbstract:
SUMMARYThe relevance of spatial variation in the environment and host communities for parasite community composition is poorly documented, creating a need for additional case studies from which general principles can be developed. Avian malaria in southern African waterfowl has not previously been studied. As a first step towards documenting and understanding its biogeography, we used PCR and molecular sequencing techniques to analyse 454 blood samples from Afrotropical ducks from 5 different locations (spread around the subregion) for avian malaria. Fifty-five blood samples were positive for one or more genera of haematozoa. The regional infection rate across all sites and sampling periods was 12·1%. Nine individuals carried dual infections containing multiple haematozoa. Fifteen different cytochrome b haplotypes among 52 positives (3 samples failed to sequence) and 61 total sequences were found. Eleven haplotypes closely matched Plasmodium, whereas 4 were more similar to Haemoproteus. Five distinct haematozoan clades were identified. Haemoproteus parasites appeared to be more host-specific than Plasmodium, which occurred at every sampling location and in every host species examined. There were no significant differences in overall parasite prevalence attributable to either site or species, although Plasmodium and Haemoproteus occurrences differed by site-species combination and the borderline significance of our test for between-site variation (P < 0·06) implied that with a larger sample size, differences in parasite prevalence among locations might be detectable.
31
Morozov, Pavel, Tatyana Sitnikova, Gary Churchill, Francisco José Ayala, and Andrey Rzhetsky. "A New Method for Characterizing Replacement Rate Variation in Molecular Sequences: Application of the Fourier and Wavelet Models to Drosophila and Mammalian Proteins." Genetics 154, no. 1 (January 1, 2000): 381–95. http://dx.doi.org/10.1093/genetics/154.1.381.
Full textAbstract:
Abstract We propose models for describing replacement rate variation in genes and proteins, in which the profile of relative replacement rates along the length of a given sequence is defined as a function of the site number. We consider here two types of functions, one derived from the cosine Fourier series, and the other from discrete wavelet transforms. The number of parameters used for characterizing the substitution rates along the sequences can be flexibly changed and in their most parameter-rich versions, both Fourier and wavelet models become equivalent to the unrestricted-rates model, in which each site of a sequence alignment evolves at a unique rate. When applied to a few real data sets, the new models appeared to fit data better than the discrete gamma model when compared with the Akaike information criterion and the likelihood-ratio test, although the parametric bootstrap version of the Cox test performed for one of the data sets indicated that the difference in likelihoods between the two models is not significant. The new models are applicable to testing biological hypotheses such as the statistical identity of rate variation profiles among homologous protein families. These models are also useful for determining regions in genes and proteins that evolve significantly faster or slower than the sequence average. We illustrate the application of the new method by analyzing human immunoglobulin and Drosophilid alcohol dehydrogenase sequences.
32
Bauerle, W. L., T. H. Whitlow, T. L. Setter, and F. M. Vermeylen. "Abscisic Acid Synthesis in Acer rubrum L. Leaves—A Vapor-pressure-deficit-mediated Response." Journal of the American Society for Horticultural Science 129, no. 2 (March 2004): 182–87. http://dx.doi.org/10.21273/jashs.129.2.0182.
Full textAbstract:
Quantitative differences in leaf abscisic acid (ABA) among Acer rubrum L. (red maple) ecotypes were investigated. This study tested the hypothesis that seedlings from wet and dry maternal sites display distinctly different capacities to synthesize ABA in response to atmospheric vapor pressure deficits. The increased levels of ABA in leaf tissue in the red maple ecotypes were associated with atmospheric vapor pressure deficit (VPD). Leaves on well-watered plants responded to VPD by increasing their ABA levels and reducing their photosynthesis (Anet) and stomatal conductance (gs). Both ecotypes appear to accumulate ABA at about the same rate as VPD increased. Despite the similar accumulation rates between ecotypes, wet site ecotypes consistently had a higher level of ABA present in leaf tissue under both low and high VPD conditions. Furthermore, wet site provenances appear to reduce Anet and gs in response to ABA accumulation, whereas dry sites do not present as clear an ABA/gs relationship. This study shows variation between wet and dry site red maple populations in physiological response to atmospheric vapor pressure deficits, indicating that natural ecotypic variation in stomatal responsiveness to air humidity is likely mediated by ABA accumulation in leaf tissue. This research demonstrates that ecotypes of red maple may be selected for atmospheric drought tolerance based on site moisture conditions.
33
Noble, Robert, Oliver Kaltz, and Michael E. Hochberg. "Peto's paradox and human cancers." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1673 (July 19, 2015): 20150104. http://dx.doi.org/10.1098/rstb.2015.0104.
Full textAbstract:
Peto's paradox is the lack of the expected trend in cancer incidence as a function of body size and lifespan across species. The leading hypothesis to explain this pattern is natural selection for differential cancer prevention in larger, longer lived species. We evaluate whether a similar effect exists within species, specifically humans. We begin by reanalysing a recently published dataset to separate the effects of stem cell number and replication rate, and show that each has an independent effect on cancer risk. When considering the lifetime number of stem cell divisions in an extended dataset, and removing cases associated with other diseases or carcinogens, we find that lifetime cancer risk per tissue saturates at approximately 0.3–1.3% for the types considered. We further demonstrate that grouping by anatomical site explains most of the remaining variation. Our results indicate that cancer risk depends not only on the number of stem cell divisions but varies enormously (approx. 10 000 times) depending on anatomical site. We conclude that variation in risk of human cancer types is analogous to the paradoxical lack of variation in cancer incidence among animal species and may likewise be understood as a result of evolution by natural selection.
34
Carulli, J. P., and D. L. Hartl. "Variable rates of evolution among Drosophila opsin genes." Genetics 132, no. 1 (September 1, 1992): 193–204. http://dx.doi.org/10.1093/genetics/132.1.193.
Full textAbstract:
Abstract DNA sequences and chromosomal locations of four Drosophila pseudoobscura opsin genes were compared with those from Drosophila melanogaster, to determine factors that influence the evolution of multigene families. Although the opsin proteins perform the same primary functions, the comparisons reveal a wide range of evolutionary rates. Amino acid identities for the opsins range from 90% for Rh2 to more than 95% for Rh1 and Rh4. Variation in the rate of synonymous site substitution is especially striking: the major opsin, encoded by the Rh1 locus, differs at only 26.1% of synonymous sites between D. pseudoobscura and D. melanogaster, while the other opsin loci differ by as much as 39.2% at synonymous sites. Rh3 and Rh4 have similar levels of synonymous nucleotide substitution but significantly different amounts of amino acid replacement. This decoupling of nucleotide substitution and amino acid replacement suggests that different selective pressures are acting on these similar genes. There is significant heterogeneity in base composition and codon usage bias among the opsin genes in both species, but there are no consistent relationships between these factors and the rate of evolution of the opsins. In addition to exhibiting variation in evolutionary rates, the opsin loci in these species reveal rearrangements of chromosome elements.
35
Wong, JLC, CWY Ho, G. Scott, JT Machin, and TWR Briggs. "Getting It Right First Time: the national survey of surgical site infection rates in NHS trusts in England." Annals of The Royal College of Surgeons of England 101, no. 7 (September 2019): 463–71. http://dx.doi.org/10.1308/rcsann.2019.0064.
Full textAbstract:
Introduction Surgical site infections are associated with increased morbidity and mortality in patients. The Getting It Right First Time surgical site infection programme set up a national survey to review surgical site infection rates in surgical units in England. The objectives were for frontline clinicians to assess the rates of infection following selected procedures, to examine the risk of significant complications and to review current practice in the prevention of surgical site infection. Methods A national survey was launched in April 2017 to assess surgical site infections within 13 specialties: breast surgery, cardiothoracic surgery, cranial neurosurgery, ear, nose and throat surgery, general surgery, obstetrics and gynaecology, ophthalmology, oral and maxillofacial surgery, orthopaedic surgery, paediatric surgery, spinal surgery, urology and vascular surgery. All participating trusts prospectively identified and collected supporting information on surgical site infections diagnosed within the six-month study period. Results Data were received from 95 NHS trusts. A total of 1807 surgical site infection cases were reported. There were variations in rates reported by trusts across specialties and procedures. Reoperations were reported in 36.2% of all identified cases, and surgical site infections are associated with a delayed discharge rate of 34.1% in our survey. Conclusion The Getting It Right First Time surgical site infection programme has introduced a different approach to infection surveillance in England. Results of the survey has demonstrated variation in surgical site infection rates among surgical units, raised the importance in addressing these issues for better patient outcomes and to reduce the financial burden on the NHS. Much work remains to be done to improve surgical site infection surveillance across surgical units and trusts in England.
36
Gielens, Grahame, Sandra Gillespie, Lisa Neame, and Elizabeth Elle. "Pollen limitation is uncommon in an endangered oak savannah ecosystem." Botany 92, no. 10 (October 2014): 743–48. http://dx.doi.org/10.1139/cjb-2014-0054.
Full textAbstract:
Pollen receipt limits reproduction in many plants, potentially affecting population viability and trait evolution. Despite considerable research, there is little consensus on the causes of pollen limitation (PL). Reviews suggest spatial and temporal variation in PL may be important for plant reproductive fitness, yet few studies have examined PL in multiple species across sites and years. We examined how pollinator communities affected PL in six wildflower species across six sites and 2 years. Although our study was conducted in a fragmented ecosystem and on perennial species (both are associated with PL in meta-analyses), we found that PL was uncommon. The degree of PL was highly variable among years, sites, and species, with no species or site showing consistent PL. Variation in PL among sites and years was not explained by variation in diversity or visit rate of the pollinating fauna. The rarity of PL in this study may limit our assessment of the importance of pollinators, but our results do suggest that PL is highly context-dependent, which should be a focus for future work.
37
Yang, Ziheng. "Statistical Properties of a DNA Sample Under the Finite-Sites Model." Genetics 144, no. 4 (December 1, 1996): 1941–50. http://dx.doi.org/10.1093/genetics/144.4.1941.
Full textAbstract:
Statistical properties of a DNA sample from a random-mating population of constant size are studied under the finite-sites model. It is assumed that there is no migration and no recombination occurs within the locus. A Markov process model is used for nucleotide substitution, allowing for multiple substitutions at a single site. The evolutionary rates among sites are treated as either constant or variable. The general likelihood calculation using numerical integration involves intensive computation and is feasible for three or four sequences only; it may be used for validating approximate algorithms. Methods are developed to approximate the probability distribution of the number of segregating sites in a random sample of n sequences, with either constant or variable substitution rates across sites. Calculations using parameter estimates obtained for human D-loop mitochondrial DNAs show that among-site rate variation has a major effect on the distribution of the number of segregating sites; the distribution under the finite-sites model with variable rates among sites is quite different from that under the infinite-sites model.
38
Sullivan, Jack, and David L. Swofford. "Should We Use Model-Based Methods for Phylogenetic Inference When We Know That Assumptions About Among-Site Rate Variation and Nucleotide Substitution Pattern Are Violated?" Systematic Biology 50, no. 5 (September 1, 2001): 723–29. http://dx.doi.org/10.1080/106351501753328848.
Full text
39
Passoni, José Carlos, Maria Lúcia Benozzati, and Miguel Tréfaut Rodrigues. "Mitochondrial DNA polymorphism and heteroplasmy in populations of the three species of Tropidurus of the nanuzae group (Squamata, Tropiduridae)." Genetics and Molecular Biology 23, no. 2 (June 2000): 351–56. http://dx.doi.org/10.1590/s1415-47572000000200019.
Full textAbstract:
The nanuzae group of lizards includes three species, Tropidurus nanuzae, T. divaricatus and T. amathites. The first species is found along Serra do Espinhaço, in eastern Brazil, and the other two in the northern region of the Brazilian State of Bahia, in continental dunes on both margins of the São Francisco River. Restriction fragment length polymorphisms (RFLP) of the mtDNA in these species were detected in 53 restriction sites. Site and fragment length polymorphisms were characterized, and cases of heteroplasmy involving length variation were observed. In T. divaricatus, these variations involved changes of 50-200 bp, probably in the control region of the molecule. In T. amathites, variation was apparently due to duplication/deletion of a 400-bp segment. Fragment length mutation rate varied among the species, being smaller in T. amathites than in T. divaricatus. Relatively low nucleotide diversity values were detected in these populations, the smallest being found in T. nanuzae. The most polymorphic population was T. divaricatus from Alagoado, followed by that of the same species from Ibiraba, suggesting both probable recovery of mtDNA genetic diversity after putative reductions in population size, and recent population expansion.
40
Grenat, Pablo R., Julián A. Valetti, and Adolfo L. Martino. "Intra-specific variation in advertisement call of Odontophrynus cordobae (Anura, Cycloramphidae): a multilevel and multifactor analysis." Amphibia-Reptilia 34, no. 4 (2013): 471–82. http://dx.doi.org/10.1163/15685381-00002902.
Full textAbstract:
Advertisement call is a complex signal that can vary at different scales and the characterization of this variation is crucial to understand its adaptive function. In our study, we examined different factors that could influence intra and inter-population call variation in Odontophrynus cordobae. We analyzed calls of individuals from different breeding sites across the species distribution, including a syntopic site with their related species O. americanus. Dominant frequency, pulse rate, call duration and pulses/call were the acoustic parameters that showed the lowest intra-individual variation (CV ≤ 3%). The discriminant function analysis (DFA) assigned 92% of calls to the correct individual, indicating that the advertisement calls of O. cordobae are individually distinctive. Univariate and multivariate statistical analysis showed a significant contribution of pulse rate in differentiation of populations. Interpulse interval and pulse rate showed a moderate clinal variation, even when syntopic populations were excluded from the analysis. We found no association between acoustic and linear geographical or altitudinal distances and observed an evident divergence between the syntopic population and the other populations analyzed. This result is reinforced by DFA, which showed a differentiation among syntopic and allopatric populations of O. cordobae. We discuss our results from the hypothesis of a possible character displacement influencing call properties in this species in syntopy with their related species O. americanus. However, new syntopic areas and tests of female preferences would be needed to strengthen our results.
41
Stanton, Brian J. "Clonal variation in basal area growth patterns during stand development in hybrid poplar." Canadian Journal of Forest Research 31, no. 12 (December 1, 2001): 2059–66. http://dx.doi.org/10.1139/x01-150.
Full textAbstract:
Two-year periodic basal area increments (PBAI) of short-rotation Populus stands were followed through a 6-year rotation in monoclonal plots at three sites to assess variation in response patterns among 20 Populus trichocarpa Torr. & Gray × Populus deltoides Bartr. clones. Data were analyzed using a split-plot model for repeated measurements with the main effect of time and the time × clone interaction partitioned into their linear and quadratic orthogonal components. The form of the mean clone growth response was mainly quadratic with PBAI culminating during the second period at 145160% of the rotation mean. Increments fell to 95116% of the rotation mean during the following period. Response variation occurred mainly in the degree of linearity at two sites with clones varying in the rate of growth deceleration during the third period, while quadratic response variation was of prime importance at the third site. Changes in basal area levels among the topmost clones over the last stage of stand development were associated with the divergence in the linear and quadratic responses. Selection on the basis of interaction contrasts of periodic growth from monoclonal plot trials is discussed in terms of sustaining yield improvements and maintaining adaptation to short rotation strategies.
42
Stojnic, Srdjan, Sasa Orlovic, Andrej Pilipovic, Dragica Vilotic, Mirjana Sijacic-Nikolic, and Danijela Miljkovic. "Variation in leaf physiology among three provenances of European beech (Fagus sylvatica L.) in provenance trial in Serbia." Genetika 44, no. 2 (2012): 341–53. http://dx.doi.org/10.2298/gensr1202341s.
Full textAbstract:
The paper presents the results of investigation of variability of net photosynthesis (A), transpiration (E), stomatal conductance (gs) and water use efficiency (WUE) of three European beech (Fagus sylvatica L.) provenances in the provenance trial established on Fruska Gora Mt. Provenances originate from three localities along a gradient from the north to the south of Europe: Pfalzgrafenweiler (Germany), Grenchen (Swiss) and Valkonya (Hungary). Results indicate that observed parameters were influenced both by environmental conditions of sites and genetic constitution of provenances. On the basis of ANOVA procedure it was observed significant differences among provenances in terms of rate of transpiration (p_0.037) and water use efficiency (p_0.011), while differences regarding net photosynthesis and stomatal conductance were not statistically significant. Canonical discriminant analysis (CDA) was performed in order to estimate multivariate relations among analyzed physiological parameters. Provenances were separated by the first canonical axis (CD1), which described 96.4% of variability. Provenance from the driest site (Valkonya) showed the highest water use efficiency, indicating on high potential for afforestation programmes in more arid areas.
43
Kaefer, Igor Luis, and Albertina Pimentel Lima. "Sexual signals of the Amazonian frog Allobates paleovarzensis: geographic variation and stereotypy of acoustic traits." Behaviour 149, no. 1 (2012): 15–33. http://dx.doi.org/10.1163/156853912x623757.
Full textAbstract:
AbstractBecause of its close relationship with the process of evolutionary differentiation, it is expected that geographic variability in acoustic sexual traits should be greater among than within populations. This is particularly expected in organisms with typically high population genetic structure and low dispersal abilities, such as anuran amphibians. We studied the acoustic traits of the advertisement call in the small-sized dendrobatoid frog Allobates paleovarzensisthrough its range in Central Amazonia. We accessed the variability of call traits from the within-male to the among-population levels, and evaluated the degree of stereotypy of the call characteristics. Call variability had comparable magnitudes within and among populations, and was independent of the degree of stereotypy of call measurements. Therefore, none of the call traits stood out as a potential cue for discrimination between populations. Spectral call measurements were static and strongly related with body size, which explained between 30 and 35% of the variation of these acoustic traits. Temporal characters of the notes were dynamic and influenced by environmental temperature (e.g., 27% of note rate variation), whilst temporal measurements of the entire calls were not related to the co-factors analysed. Both spectral and temporal call traits varied among populations and between sides of the Amazon River. Our results also indicate that body size and sampling site jointly affected the variability of the call traits. However, geographic distances among populations and the river barrier had no significant effect on the overall acoustic variation, indicating that local stabilising selective forces may be important in the process of call differentiation.
44
Zhang, Ming Li, Ming Gao, Biao Xie, and Hao Yang. "Estimating Medium-Term Soil Erosion Rates under Different Types of Land Use in Red Soil Region of Jiangxi, Southern China Using 137Cs Technique." Advanced Materials Research 518-523 (May 2012): 4716–20. http://dx.doi.org/10.4028/www.scientific.net/amr.518-523.4716.
Full textAbstract:
Soil erosion has been recognized as one of the major environmental problem in red soil region of southern China. The spatial variation of soil erosion was studied using 137Cs technique at three sites (site A, site B, site C) under different type of land use in Jiangxi province. To understand the spatial distribution of soil erosion is important for taking proper soil and water conservation measures. 280 samples were collected at three sites. Medium-term average soil erosion rates estimated for dry farmland is 83.1 kg ha-1 a-1 at site A, and that for paddy fields with terraces on the middle-lower slope is 79.2 kg ha-1 a-1 at site B. Among the uncultivated lands, the average soil erosion rate of bare land is 3700 kg ha-1 a-1 on the upper slope at site A, that of woodland covered with masson pines on the upper slope is 1106 kg ha-1 a-1 at site B and that of economic forest that covered with orchard is 1380.5 kg ha-1 a-1 at site C. On the whole, the soil erosion rate of cultivated land is lower than that of uncultivated land. Bare land, woodland and orchard are the three main sources of soil erosion in red soil region of southern China. Protective measures of cultivated land, such as terraces, field ridge and ditch beside the land, had been demonstrated effectively in controlling soil erosion. The findings provide more information on agricultural land under different type of land use and managed measures which play an important role in controlling the soil loss in Southern China to a certain degree.
45
Payment, Pierre, Aminata Berte, and Carole Fleury. "Sources of variation in isolation rate of Giardia lamblia cysts and their homogeneous distribution in river water entering a water treatment plant." Canadian Journal of Microbiology 43, no. 7 (July 1, 1997): 687–89. http://dx.doi.org/10.1139/m97-098.
Full textAbstract:
The objective of this work was to determine if differences in the number of Giardia cysts measured in river water were due to the method itself, the analyst, or real differences in the distribution of these cysts in water. To minimize the methodological differences, centrifugation only was used as the primary concentration method. Differences were observed between results from different analysts and they were identified as technical errors. Once the method had been well established, cysts were found to be distributed homogeneously in the river water tested. Small differences were observed among samples collected sequentially at the same time, as well as for samples collected on different days or at different times on the same day. The differences reported in the literature in the number of Giardia cysts detected in water samples from the same site could be an artifact of the methods more than true differences in the counts.Key words: water, Giardia, parasite, methods.
46
Pearce, John M., and Sandra L. Talbot. "Demography, Genetics, and the Value of Mixed Messages." Condor 108, no. 2 (May 1, 2006): 474–79. http://dx.doi.org/10.1093/condor/108.2.474.
Full textAbstract:
Abstract Iverson et al. (2004) used estimates of the homing rate for molting adult Harlequin Ducks (Histrionicus histrionicus) in Alaska to draw inferences about population structure. Homing rates, defined as one minus the ratio of birds recaptured elsewhere to those recaptured at the original banding site, were high (0.95–1.00) for males and females. Iverson et al. (2004) concluded that these high rates of homing are indicative of demographic independence among molting groups separated by small distances (tens to hundreds of kilometers) and that conservation efforts should recognize this fine-scale population structure. We re-examined their use of the homing rate, because their assumption of equal detection probability across a wide sampling area could have led to an upward bias in their estimates of site fidelity. As a result, we are hesitant to agree with their conclusion of high adult homing to molting areas and that molt-site fidelity is evidence for demographic independence. Our hesitancy stems from the fact that little is known about juvenile and adult movements within and among years, breeding area origins, and the variation of demographic parameters (e.g., survival and productivity) among molting groups. Furthermore, population genetic data of these molting groups suggest gene flow at both nuclear and mitochondrial loci. Such mixed messages between demographic (i.e., banding) and genetic data are increasingly common in ornithological studies and offer unique opportunities to reassess predictions and make more robust inferences about population structure across broad temporal and spatial scales. Thus, we stress that it is this broader scale perspective, which combines both demography and genetics, that biologists should seek to quantify and conservation efforts should seek to recognize.
47
Virgo, K. S., S. Sarkar, A. L. Beitler, J. F. Gibbs, K. Sakata, A. Goel, M. E. Christy, R. A. Audisio, W. G. Kraybill, and F. E. Johnson. "Geographic variation in soft tissue sarcoma patient follow-up." Journal of Clinical Oncology 25, no. 18_suppl (June 20, 2007): 20518. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.20518.
Full textAbstract:
20518 Background: Of all newly diagnosed malignancies, 1% are soft tissue sarcomas (STS) and 59% of STS occur in the extremities. Most patients (80%) suffer recurrence within two years of potentially curative resection. Late recurrences at five years and beyond are not uncommon. Surveillance programs are designed to identify recurrence or new primaries early enough to positively impact survival and quality of life. Though published guidelines exist for extremity STS follow-up, adherence varies among physicians. Geographic factors were hypothesized to be potential predictors of this variation. Methods: The SSO membership (N=1592) was surveyed regarding postoperative STS surveillance using standardized clinical vignettes. Practice patterns were analyzed by metropolitan statistical area (MSA), managed care organization (MCO) penetration rate, and U.S. census region using repeated measures analysis of variance. The study endpoint was surveillance intensity. Results: Forty-five percent of SSO members (714) completed the survey; 343 (48%) performed sarcoma surgery. Of those who perform surgery, 318 (93%) follow their patients long-term. Mean follow-up intensity for the 12 modalities was highly correlated by tumor size, grade, and years after surgery. Controlling for tumor stage, grade, and year after surgery, geographic factors infrequently predicted surgeon self-reported surveillance intensity (p < .05). MSA was a significant predictor of office visit frequency. MCO penetration rate significantly predicted the frequency of urinalysis and site MRI. U.S. census region significantly predicted the frequency of LFTs. Two-way interaction effects were frequently significant. Few three-way interactions were examined due to sample size limitations. Conclusion: Geographic factors were generally not predictive of surgeon self-reported surveillance practice patterns for patients after curative-intent sarcoma surgery. Internship, residency, and fellowship locations may be important surgeon-specific aspects for future surveys. No significant financial relationships to disclose.
48
Williams, Tony D., Nils Warnock, John Y. Takekawa, and Mary Anne Bishop. "Flyway-Scale Variation in Plasma Triglyceride Levels as an Index of Refueling Rate in Spring-Migrating Western Sandpipers (Calidris Mauri)." Auk 124, no. 3 (July 1, 2007): 886–97. http://dx.doi.org/10.1093/auk/124.3.886.
Full textAbstract:
Abstract We combined radiotelemetry, plasma metabolite analyses, and macro-invertebrate prey sampling to investigate variation in putative fattening rates (estimated as plasma triglyceride levels) at the flyway scale in Western Sandpipers (Calidris mauri) migrating between Punta Banda, Mexico (31°N), and Hartney Bay, Alaska (60°N), a distance of 4,240 km. Birds were caught at a wintering site (San Francisco Bay) and eight stopover sites along this Pacific Flyway. Body mass was higher in females than in males at six sites, but variation was not correlated with latitude for either sex, and the relationship of change in mass by date within sites was uninformative with regard to possible latitudinal variation in fattening rates. At San Francisco Bay, triglyceride levels were higher in the spring than in the winter. Mean plasma triglyceride varied among stopover sites, and there was a significant linear trend of increasing triglyceride levels with latitude as birds migrated north. At San Francisco Bay, length of stay was negatively related to triglyceride levels. However, plasma triglyceride levels at wintering or initial stopover sites (San Francisco and Punta Banda) did not predict individual variation in subsequent rates of travel during migration. We found no significant relationship between triglyceride levels and prey biomass at different stopover sites, which suggests that the latitudinal pattern is not explained by latitudinal changes in food availability. Rather, we suggest that differences in physiology of migratory birds at southern versus northern stopover sites or behavioral differences may allow birds to sustain higher fattening rates closer to the breeding grounds. Variación a la Escala de Corredores de Vuelo en los Niveles de Triglicéridos Plasmáticos como un Índice de la Tasa de Reabastecimiento durante la Migración de Primavera en Calidris mauri
49
Hansen, Rikke Reisner, Oskar Liset Pryds Hansen, Joseph J. Bowden, Urs A. Treier, Signe Normand, and Toke Høye. "Meter scale variation in shrub dominance and soil moisture structure Arctic arthropod communities." PeerJ 4 (July 14, 2016): e2224. http://dx.doi.org/10.7717/peerj.2224.
Full textAbstract:
The Arctic is warming at twice the rate of the rest of the world. This impacts Arctic species both directly, through increased temperatures, and indirectly, through structural changes in their habitats. Species are expected to exhibit idiosyncratic responses to structural change, which calls for detailed investigations at the species and community level. Here, we investigate how arthropod assemblages of spiders and beetles respond to variation in habitat structure at small spatial scales. We sampled transitions in shrub dominance and soil moisture between three different habitats (fen, dwarf shrub heath, and tall shrub tundra) at three different sites along a fjord gradient in southwest Greenland, using yellow pitfall cups. We identified 2,547 individuals belonging to 47 species. We used species richness estimation, indicator species analysis and latent variable modeling to examine differences in arthropod community structure in response to habitat variation at local (within site) and regional scales (between sites). We estimated species responses to the environment by fitting species-specific generalized linear models with environmental covariates. Species assemblages were segregated at the habitat and site level. Each habitat hosted significant indicator species, and species richness and diversity were significantly lower in fen habitats. Assemblage patterns were significantly linked to changes in soil moisture and vegetation height, as well as geographic location. We show that meter-scale variation among habitats affects arthropod community structure, supporting the notion that the Arctic tundra is a heterogeneous environment. To gain sufficient insight into temporal biodiversity change, we require studies of species distributions detailing species habitat preferences.
50
Taylor, Jolyn Sharpe, Claire Marten, Kimberly Potts, Lynn Cloutier, Katherine Cain, Shauna Fenton, Tara Tatum, et al. "What is the real rate of surgical-site infection?" Journal of Clinical Oncology 34, no. 7_suppl (March 1, 2016): 171. http://dx.doi.org/10.1200/jco.2016.34.7_suppl.171.
Full textAbstract:
171 Background: Surgical site infections (SSI) are associated with patient morbidity and increased healthcare costs. Although several national organizations monitor SSI including the University Health System Consortium (UHC), National Surgical Quality Improvement Program (NSQIP), National Healthcare Safety Network (NHSN) and Agency for Healthcare Research and Quality (AHRQ), there is no standard reporting methodology. We compared SSI rates from these databases to our own chart review. Methods: We queried the UHC, NSQIP, NHSN and AHRQ databases from 7/2012-6/2014 for SSI following gynecologic surgery at our institution. UHC and AHRQ rely on ICD-9 coding while NSQIP and NHSN employ trained reviewers. Each organization uses different definitions, inclusion and exclusion criteria for SSI. NSQIP reviews 13-17% of cases at our institution while the other agencies include all cases. The rate of SSI was also obtained from chart review for 5/1/2014-6/30/2014 with SSI defined as an infection of the surgical incision or organ space requiring antibiotics. SSI was classified as superficial, deep or organ space (OS). The rates reported by the agencies were compared to the rate obtained by chart review using Fisher’s exact test. Results: The combined UHC/NSQIP/NHSN/AHRQ SSI rate was 5.1% (78/1,540) while the rate found by chart review was 12% (20/166) (p = 0.001). Overall SSI rates for the databases were: UHC 1.6%, NSQIP 8.8%, NHSN 2.9% and AHRQ < 1%. The combined database reported fewer superficial SSI compared to investigator chart review but did not differ significantly when reporting deep and OS: superficial 1.6% v 7.8% (p < 0.001), deep 2.1% v 1.2% (p = 0.57) and OS 2.9% v 3.6% (p = 0.26). The individual databases had wide variation in rate of superficial (UHC 0.7% NSQIP 1.2% NHSN 0.5% AHRQ 0%), deep (UHC 0.7% NSQIP 4.7% NHSN 1.3% AHRQ 0%) and OSI (UHC 0.03% NSQIP 4.4% NHSN 1.4% AHRQ < 1%). Only 19 cases (24.4%) were included in > 1 database. Only one case was included in three databases (1.3%) and no cases were included in all four. Conclusions: There is discordance among national reporting agencies tracking SSI and all agencies reported a different rate of SSI compared to chart review. Adopting standardized metrics across agencies could improve consistency and accuracy in assessing SSI rates.