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1.
PLoS One ; 15(11): e0242873, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33227027

RESUMO

The animal-human relationship is essential for farm animal welfare and production. Generally, gentle tactile and vocal interactions improve the animal-human relationship in cattle. However, cows that are fearful of humans avoid their close presence and touch; thus, the animal-human relationship first has to be improved to a point where the animals accept stroking before their perception of the interactions and consequently the animal-human relationship can become positive. We tested whether the animal-human relationship of cows fearful of humans is improved more effectively by gentle interactions during restraint, allowing physical contact from the beginning, or if the gentle interactions are offered while the animals are free to move, giving them more control over the situation and thus probably a higher level of agency and a more positive perception of the interactions. Thirty-six dairy cows (median avoidance distance 1.6 m) were assigned to three treatments (each n = 12): gentle vocal and tactile interactions during restraint in the feeding rack (LOCK); gentle vocal and, if possible, tactile interactions while free in the barn (FREE); routine management without additional interactions (CON). Treatments were applied for 3 min per cow on 10 d per fortnight for 6 weeks (i.e., three periods). Avoidance and approach behaviour towards humans was tested before the start of the treatment period, and then at 2-week intervals. The recorded variables were reduced to one score by Principal Component Analysis. The resulting relationship score (higher values implying a better relationship with humans) increased in all groups; the increase was stronger in FREE than in CON, with the increase in LOCK being not significantly different from the other treatment groups. Thus, we recommend that gentle interactions with cows should take place while they are unrestrained, if possible.

2.
Front Psychol ; 11: 579346, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33178082

RESUMO

The quality of the animal-human relationship and, consequently, the welfare of animals can be improved by gentle interactions such as stroking and talking. The perception of different stimuli during these interactions likely plays a key role in their emotional experience, but studies are scarce. During experiments, the standardization of verbal stimuli could be increased by using a recording. However, the use of a playback might influence the perception differently than "live" talking, which is closer to on-farm practice. Thus, we compared heifers' (n = 28) reactions to stroking while an experimenter was talking soothingly ("live") or while a recording of the experimenter talking soothingly was played ("playback"). Each animal was tested three times per condition and each trial comprised three phases: pre-stimulus, stimulus (stroking and talking) and post-stimulus. In both conditions, similar phrases with positive content were spoken calmly, using long low-pitched vowels. All tests were video recorded and analyzed for behaviors associated with different affective states. Effects on the heifers' cardiac parameters were assessed using analysis of heart rate variability. Independently of the auditory stimuli, longer durations of neck stretching occurred during stroking, supporting our hypothesis of a positive perception of stroking. Observation of ear positions revealed longer durations of the "back up" position and less ear flicking and changes of ear positions during stroking. The predicted decrease in HR during stroking was not confirmed; instead we found a slightly increased mean HR during stroking with a subsequent decrease in HR, which was stronger after stroking with live talking. In combination with differences in HRV parameters, our findings suggest that live talking might have been more pleasurable to the animals and had a stronger relaxing effect than "playback." The results regarding the effects of the degree of standardization of the stimulus on the variability of the data were inconclusive. We thus conclude that the use of recorded auditory stimuli to promote positive affective states during human-animal interactions in experimental settings is possible, but not necessarily preferable.

3.
Animals (Basel) ; 10(3)2020 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-32143274

RESUMO

Gentle animal-human interactions, such as stroking, can promote positive emotions and thus welfare in cattle. While previous studies showed that stroking at the ventral neck elicited the most positive reactions in cows, intra-specific allogrooming in cattle includes different body regions and is probably guided partly by the receiver. Thus, we compared heifers' (n = 28) reactions to stroking with the experimenter either reactively responding to perceived momentary preferences of the heifers or exclusively stroking the ventral neck. Independently of the stroking style, longer durations of neck stretching and contact occurred during stroking, supporting our hypothesis of a positive perception of stroking. We did not confirm the predicted decrease in heart rate and increase in heart rate variability, but instead found a slightly increased mean heart rate during stroking. The different stroking styles elicited differences in the heifers' ear positions: "reactive" stroking led to longer durations of low ear positions during stroking, while during "ventral neck" stroking, the duration of back up increased. However, no other behaviours differed significantly between different stroking styles, indicating that the exact manner of stroking applied in our treatments seemed to be less important in the promotion of positive affective states in cattle through gentle human-animal interactions.

4.
Animals (Basel) ; 9(9)2019 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-31491913

RESUMO

The focus of animal welfare science has shifted over the last decades from efforts to avoid negative states to ways of allowing animals the experience of positive emotions. They may influence physiological processes in farmed animals, potentially providing health benefits; in addition, the physiological changes might be used as indicators of emotional states. We investigated calves' salivary secretory immunoglobulin A (sIgA) concentrations with regard to a possible circadian rhythm and two situations that elicit positive emotions. Ten saliva samples of 14 calves were taken on two consecutive days; within the course of a day we observed a significant decline in salivary sIgA concentrations at 14:00 h. Further, we probed the animals before and after milk feeding and, contrarily to our prediction, detected lower sIgA concentrations 5 min after feeding than 15 min before. A probable explanation might be an increase in salivary flow rate caused by milk ingestion. We also took samples before and after we stimulated play behavior in calves. There was no significant difference in sIgA concentrations between samples taken before and after play. Although there was a significant correlation between the change in sIgA concentrations and the amount of play behavior shown, the correlation depended on an unexpected decrease of sIgA in animals that played little, and thus, does not support our hypothesis. In general, the data showed a large variability that might arise from different factors that are difficult to standardize in animals. Thus, the use of salivary sIgA concentrations as a marker of positive emotions in calves is not supported conclusively by the present data.

5.
Genome Biol ; 20(1): 169, 2019 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-31416462

RESUMO

BACKGROUND: The combination of experimental evolution with whole-genome resequencing of pooled individuals, also called evolve and resequence (E&R) is a powerful approach to study the selection processes and to infer the architecture of adaptive variation. Given the large potential of this method, a range of software tools were developed to identify selected SNPs and to measure their selection coefficients. RESULTS: In this benchmarking study, we compare 15 test statistics implemented in 10 software tools using three different scenarios. We demonstrate that the power of the methods differs among the scenarios, but some consistently outperform others. LRT-1, CLEAR, and the CMH test perform best despite LRT-1 and the CMH test not requiring time series data. CLEAR provides the most accurate estimates of selection coefficients. CONCLUSION: This benchmark study will not only facilitate the analysis of already existing data, but also affect the design of future data collections.


Assuntos
Benchmarking , Seleção Genética , Análise de Sequência de DNA , Software , Animais , Simulação por Computador , Drosophila melanogaster/genética , Análise de Componente Principal
6.
Life Sci Alliance ; 2(2)2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-31023833

RESUMO

Meiotic recombination has strong, but poorly understood effects on short tandem repeat (STR) instability. Here, we screened thousands of single recombinant products with sperm typing to characterize the role of polymorphic poly-A repeats at a human recombination hotspot in terms of hotspot activity and STR evolution. We show that the length asymmetry between heterozygous poly-A's strongly influences the recombination outcome: a heterology of 10 A's (9A/19A) reduces the number of crossovers and elevates the frequency of non-crossovers, complex recombination products, and long conversion tracts. Moreover, the length of the heterology also influences the STR transmission during meiotic repair with a strong and significant insertion bias for the short heterology (6A/7A) and a deletion bias for the long heterology (9A/19A). In spite of this opposing insertion-/deletion-biased gene conversion, we find that poly-A's are enriched at human recombination hotspots that could have important consequences in hotspot activation.


Assuntos
Troca Genética/genética , Heterozigoto , Meiose/genética , Repetições de Microssatélites/genética , Poli A/genética , Alelos , Conversão Gênica/genética , Genótipo , Haplótipos/genética , Humanos , Masculino , Instabilidade de Microssatélites , Taxa de Mutação , Polimorfismo de Nucleotídeo Único/genética , Espermatozoides/citologia , Doadores de Tecidos
7.
Mol Ecol Resour ; 19(3): 623-638, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30666785

RESUMO

As recombination plays an important role in evolution, its estimation and the identification of hotspot positions is of considerable interest. We propose a novel approach for estimating population recombination rates based on genotyping or sequence data that involves a sequential multiscale change point estimator. Our method also permits demography to be taken into account. It uses several summary statistics within a regression model fitted on suitable scenarios. Our proposed method is accurate, computationally fast, and provides a parsimonious solution by ensuring a type I error control against too many changes in the recombination rate. An application to human genome data suggests a good congruence between our estimated and experimentally identified hotspots. Our method is implemented in the R-package LDJump, which is freely available at https://github.com/PhHermann/LDJump.


Assuntos
Biologia Computacional/métodos , Genética Populacional/métodos , Recombinação Genética , Técnicas de Genotipagem/métodos , Humanos , Análise de Sequência de DNA/métodos
8.
Stat Methods Med Res ; 28(8): 2292-2304, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-29635962

RESUMO

Global hypothesis tests are a useful tool in the context of clinical trials, genetic studies, or meta-analyses, when researchers are not interested in testing individual hypotheses, but in testing whether none of the hypotheses is false. There are several possibilities how to test the global null hypothesis when the individual null hypotheses are independent. If it is assumed that many of the individual null hypotheses are false, combination tests have been recommended to maximize power. If, however, it is assumed that only one or a few null hypotheses are false, global tests based on individual test statistics are more powerful (e.g. Bonferroni or Simes test). However, usually there is no a priori knowledge on the number of false individual null hypotheses. We therefore propose an omnibus test based on cumulative sums of the transformed p-values. We show that this test yields an impressive overall performance. The proposed method is implemented in an R-package called omnibus.


Assuntos
Modelos Estatísticos , Resultados Negativos/estatística & dados numéricos , Projetos de Pesquisa , Simulação por Computador , Glioma/tratamento farmacológico , Glioma/radioterapia , Humanos , Metanálise como Assunto
9.
J Alzheimers Dis ; 63(1): 103-114, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29614643

RESUMO

BACKGROUND: Comprehensive studies on caregiver burden (CB) of persons caring for dementia patients differ methodologically and show variable results. OBJECTIVE: Analysis of known and hypothesized factors of CB in home care of dementia patients. METHODS: Multicenter longitudinal study comprising 585 persons caring mostly for Alzheimer's disease patients (age median 77.25 years, Mini-Mental State Examination raw score median 23) using the Zarit Caregiver Burden Interview (CBI). Known patient-related determinants of CB were studied, such as dementia severity (Clinical Dementia Rating, CDR), neuropsychological deficits (CERAD-Plus), neuropsychiatric symptoms (Neuropsychiatric Inventory, NPI), disability (Disability Assessment for Dementia, DAD), dependency (Dependency Scale, DS), and moreover, unclarified potential factors (age, sex, education of patients; age, sex, occupational status of the caregivers; family relationship). Psychological and somatic effects of CB were analyzed (factor analysis). RESULTS: Caregiver age was median 61. Female caregivers prevailed (67.8%). Median CBI sum score (CBIss) was 16 at baseline. After two years, CBIss was 22 and 37% of the caregivers reported mild to moderate (CBIss 21-40), 16.8% moderate to severe or severe (≥41), and 46.2% absent to little CB (CBIss ≤ 20). CB correlated positively with NPI, CDR, DS scores, disability (DAD), years of education of the patients, and proximity of patient and caregiver sex (female), and negatively with caregiver age. Caregivers reported restrictions of time, health problems, and negative emotions. CONCLUSION: The findings are applicable to identify persons at risk for substantial CB and its consequences. There is demand for personal, psychological, and medical support of caregivers and increasing male participation.


Assuntos
Adaptação Psicológica , Cuidadores/psicologia , Demência/enfermagem , Serviços de Assistência Domiciliar , Idoso , Idoso de 80 Anos ou mais , Áustria/epidemiologia , Demência/diagnóstico por imagem , Demência/epidemiologia , Eletroencefalografia , Feminino , Humanos , Estudos Longitudinais , Imagem por Ressonância Magnética , Masculino , Entrevista Psiquiátrica Padronizada , Pessoa de Meia-Idade , Testes Neuropsicológicos , Escalas de Graduação Psiquiátrica , Sistema de Registros
10.
Stat Appl Genet Mol Biol ; 16(5-6): 387-405, 2017 11 27.
Artigo em Inglês | MEDLINE | ID: mdl-29095700

RESUMO

In many population genetic problems, parameter estimation is obstructed by an intractable likelihood function. Therefore, approximate estimation methods have been developed, and with growing computational power, sampling-based methods became popular. However, these methods such as Approximate Bayesian Computation (ABC) can be inefficient in high-dimensional problems. This led to the development of more sophisticated iterative estimation methods like particle filters. Here, we propose an alternative approach that is based on stochastic approximation. By moving along a simulated gradient or ascent direction, the algorithm produces a sequence of estimates that eventually converges to the maximum likelihood estimate, given a set of observed summary statistics. This strategy does not sample much from low-likelihood regions of the parameter space, and is fast, even when many summary statistics are involved. We put considerable efforts into providing tuning guidelines that improve the robustness and lead to good performance on problems with high-dimensional summary statistics and a low signal-to-noise ratio. We then investigate the performance of our resulting approach and study its properties in simulations. Finally, we re-estimate parameters describing the demographic history of Bornean and Sumatran orang-utans.


Assuntos
Genética Populacional/métodos , Funções Verossimilhança , Modelos Genéticos , Algoritmos , Teorema de Bayes , Simulação por Computador , Evolução Molecular
11.
Mol Biol Evol ; 34(11): 3023-3034, 2017 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-28961717

RESUMO

Allele frequency time series data constitute a powerful resource for unraveling mechanisms of adaptation, because the temporal dimension captures important information about evolutionary forces. In particular, Evolve and Resequence (E&R), the whole-genome sequencing of replicated experimentally evolving populations, is becoming increasingly popular. Based on computer simulations several studies proposed experimental parameters to optimize the identification of the selection targets. No such recommendations are available for the underlying parameters selection strength and dominance. Here, we introduce a highly accurate method to estimate selection parameters from replicated time series data, which is fast enough to be applied on a genome scale. Using this new method, we evaluate how experimental parameters can be optimized to obtain the most reliable estimates for selection parameters. We show that the effective population size (Ne) and the number of replicates have the largest impact. Because the number of time points and sequencing coverage had only a minor effect, we suggest that time series analysis is feasible without major increase in sequencing costs. We anticipate that time series analysis will become routine in E&R studies.


Assuntos
Adaptação Biológica/genética , Frequência do Gene/genética , Análise de Sequência de DNA/métodos , Adaptação Fisiológica/genética , Alelos , Evolução Biológica , Simulação por Computador , Evolução Molecular , Genoma , Modelos Genéticos , Polimorfismo de Nucleotídeo Único/genética , Seleção Genética , Análise de Sequência de DNA/estatística & dados numéricos , Sequenciamento Completo do Genoma/métodos
12.
Chromosome Res ; 25(2): 155-172, 2017 06.
Artigo em Inglês | MEDLINE | ID: mdl-28155083

RESUMO

PR domain containing protein 9 (PRDM9) is a meiosis-specific, multi-domain protein that regulates the location of recombination hotspots by targeting its DNA recognition sequence for double-strand breaks (DSBs). PRDM9 specifically recognizes DNA via its tandem array of zinc fingers (ZnFs), epigenetically marks the local chromatin by its histone methyltransferase activity, and is an important tether that brings the DNA into contact with the recombination initiation machinery. A strong correlation between PRDM9-ZnF variants and specific DNA motifs at recombination hotspots has been reported; however, the binding specificity and kinetics of the ZnF domain are still obscure. Using two in vitro methods, gel mobility shift assays and switchSENSE, a quantitative biophysical approach that measures binding rates in real time, we determined that the PRDM9-ZnF domain forms a highly stable and long-lived complex with its recognition sequence, with a dissociation halftime of many hours. The ZnF domain exhibits an equilibrium dissociation constant (K D) in the nanomolar (nM) range, with polymorphisms in the recognition sequence directly affecting the binding affinity. We also determined that alternative sequences (15-16 nucleotides in length) can be specifically bound by different subsets of the ZnF domain, explaining the binding plasticity of PRDM9 for different sequences. Finally, longer binding targets are preferred than predicted from the numbers of ZnFs contacting the DNA. Functionally, a long-lived complex translates into an enzymatically active PRDM9 at specific DNA-binding sites throughout meiotic prophase I that might be relevant in stabilizing the components of the recombination machinery to a specific DNA target until DSBs are initiated by Spo11.


Assuntos
Histona-Lisina N-Metiltransferase/metabolismo , Motivos de Nucleotídeos , Dedos de Zinco , Animais , Sítios de Ligação , Quebras de DNA de Cadeia Dupla , Meiose , Camundongos , Ligação Proteica , Estabilidade Proteica , Recombinação Genética
13.
Genetics ; 204(2): 723-735, 2016 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-27542959

RESUMO

The effective population size ([Formula: see text]) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term [Formula: see text] They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to [Formula: see text] Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-seq). Pool-seq is cost-effective and often outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: Additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling, which increases the variance of allele frequency estimates. We propose a new estimator of [Formula: see text] which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate [Formula: see text] estimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wide [Formula: see text] estimates, we extend our method using a recursive partitioning approach to estimate [Formula: see text] locally along the chromosome. Since the type I error is controlled, our method permits the identification of genomic regions that differ significantly in their [Formula: see text] estimates. We present an application to Pool-seq data from experimental evolution with Drosophila and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R package at https://github.com/ThomasTaus/Nest.


Assuntos
Evolução Molecular Direcionada , Frequência do Gene/genética , Densidade Demográfica , Análise de Sequência de DNA , Alelos , Animais , Drosophila/genética , Polimorfismo de Nucleotídeo Único/genética
14.
J Comput Biol ; 23(9): 756-68, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-27409412

RESUMO

The scaled recombination parameter [Formula: see text] is one of the key parameters, turning up frequently in population genetic models. Accurate estimates of [Formula: see text] are difficult to obtain, as recombination events do not always leave traces in the data. One of the most widely used approaches is composite likelihood. Here, we show that popular implementations of composite likelihood estimators can often be uniformly improved by optimizing the trade-off between bias and variance. The amount of possible improvement depends on parameters such as the sequence length, the sample size, and the mutation rate, and it can be considerable in some cases. It turns out that approximate Bayesian computation, with composite likelihood as a summary statistic, also leads to improved estimates, but now in terms of the posterior risk. Finally, we demonstrate a practical application on real data from Drosophila.


Assuntos
Algoritmos , Teorema de Bayes , Biologia Computacional/métodos , Drosophila/genética , Funções Verossimilhança , Recombinação Genética , Animais , Simulação por Computador , Modelos Genéticos , Taxa de Mutação
15.
Cell Rep ; 7(6): 2031-2041, 2014 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-24910436

RESUMO

The dynamics by which mitochondrial DNA (mtDNA) evolves within organisms are still poorly understood, despite the fact that inheritance and proliferation of mutated mtDNA cause fatal and incurable diseases. When two mtDNA haplotypes are present in a cell, it is usually assumed that segregation (the proliferation of one haplotype over another) is negligible. We challenge this assumption by showing that segregation depends on the genetic distance between haplotypes. We provide evidence by creating four mouse models containing mtDNA haplotype pairs of varying diversity. We find tissue-specific segregation in all models over a wide range of tissues. Key findings are segregation in postmitotic tissues (important for disease models) and segregation covering all developmental stages from prenatal to old age. We identify four dynamic regimes of mtDNA segregation. Our findings suggest potential complications for therapies in human populations: we propose "haplotype matching" as an approach to avoid these issues.


Assuntos
DNA Mitocondrial/genética , Sequência de Aminoácidos , Animais , Modelos Animais de Doenças , Haplótipos , Humanos , Camundongos , Modelos Genéticos , Dados de Sequência Molecular
16.
Bioinformatics ; 30(16): 2255-62, 2014 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-24753487

RESUMO

MOTIVATION: DNA segmentation, i.e. the partitioning of DNA in compositionally homogeneous segments, is a basic task in bioinformatics. Different algorithms have been proposed for various partitioning criteria such as Guanine/Cytosine (GC) content, local ancestry in population genetics or copy number variation. A critical component of any such method is the choice of an appropriate number of segments. Some methods use model selection criteria and do not provide a suitable error control. Other methods that are based on simulating a statistic under a null model provide suitable error control only if the correct null model is chosen. RESULTS: Here, we focus on partitioning with respect to GC content and propose a new approach that provides statistical error control: as in statistical hypothesis testing, it guarantees with a user-specified probability [Formula: see text] that the number of identified segments does not exceed the number of actually present segments. The method is based on a statistical multiscale criterion, rendering this as a segmentation method that searches segments of any length (on all scales) simultaneously. It is also accurate in localizing segments: under benchmark scenarios, our approach leads to a segmentation that is more accurate than the approaches discussed in the comparative review of Elhaik et al. In our real data examples, we find segments that often correspond well to features taken from standard University of California at Santa Cruz (UCSC) genome annotation tracks. AVAILABILITY AND IMPLEMENTATION: Our method is implemented in function smuceR of the R-package stepR available at http://www.stochastik.math.uni-goettingen.de/smuce.


Assuntos
Algoritmos , DNA/química , Análise de Sequência de DNA/métodos , Bacteriófago lambda/genética , Composição de Bases , Interpretação Estatística de Dados , Genoma Humano , Humanos
17.
PLoS Genet ; 9(6): e1003534, 2013 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-23754958

RESUMO

Various approaches can be applied to uncover the genetic basis of natural phenotypic variation, each with their specific strengths and limitations. Here, we use a replicated genome-wide association approach (Pool-GWAS) to fine-scale map genomic regions contributing to natural variation in female abdominal pigmentation in Drosophila melanogaster, a trait that is highly variable in natural populations and highly heritable in the laboratory. We examined abdominal pigmentation phenotypes in approximately 8000 female European D. melanogaster, isolating 1000 individuals with extreme phenotypes. We then used whole-genome Illumina sequencing to identify single nucleotide polymorphisms (SNPs) segregating in our sample, and tested these for associations with pigmentation by contrasting allele frequencies between replicate pools of light and dark individuals. We identify two small regions near the pigmentation genes tan and bric-à-brac 1, both corresponding to known cis-regulatory regions, which contain SNPs showing significant associations with pigmentation variation. While the Pool-GWAS approach suffers some limitations, its cost advantage facilitates replication and it can be applied to any non-model system with an available reference genome.


Assuntos
Drosophila melanogaster/genética , Pigmentação/genética , Locos de Características Quantitativas , Sequências Reguladoras de Ácido Nucleico/genética , Animais , Mapeamento Cromossômico , Feminino , Genética Populacional , Genoma de Inseto , Estudo de Associação Genômica Ampla , Fenótipo , Polimorfismo de Nucleotídeo Único
18.
Mol Ecol Resour ; 13(4): 740-5, 2013 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-23615333

RESUMO

Estimating differences in gene expression among alleles is of high interest for many areas in biology and medicine. Here, we present a user-friendly software tool, Allim, to estimate allele-specific gene expression. Because mapping bias is a major problem for reliable estimates of allele-specific gene expression using RNA-seq, Allim combines two different strategies to account for the mapping biases. In order to reduce the mapping bias, Allim first generates a polymorphism-aware reference genome that accounts for the sequence variation between the alleles. Then, a sequence-specific simulation tool estimates the residual mapping bias. Statistical tests for allelic imbalance are provided that can be used with the bias corrected RNA-seq data.


Assuntos
Desequilíbrio Alélico , Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Análise de Sequência de RNA/métodos
19.
Genetics ; 194(2): 473-84, 2013 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-23589457

RESUMO

Recombination is a fundamental evolutionary force. Therefore the population recombination rate ρ plays an important role in the analysis of population genetic data; however, it is notoriously difficult to estimate. This difficulty applies both to the accuracy of commonly used estimates and to the computational efforts required to obtain them. Some particularly popular methods are based on approximations to the likelihood. They require considerably less computational efforts than the full-likelihood method with not much less accuracy. Nevertheless, the computation of these approximate estimates can still be very time consuming, in particular when the sample size is large. Although auxiliary quantities for composite likelihood estimates can be computed in advance and stored in tables, these tables need to be recomputed if either the sample size or the mutation rate θ changes. Here we introduce a new method based on regression combined with boosting as a model selection technique. For large samples, it requires much less computational effort than other approximate methods, while providing similar levels of accuracy. Notably, for a sample of hundreds or thousands of individuals, the estimate of ρ using regression can be obtained on a single personal computer within a couple of minutes while other methods may need a couple of days or months (or even years). When the sample size is smaller (n ≤ 50), our new method remains computational efficient but produces biased estimates. We expect the new estimates to be helpful when analyzing large samples and/or many loci with possibly different mutation rates.


Assuntos
População/genética , Recombinação Genética , Algoritmos , Genética Populacional/métodos , Humanos , Funções Verossimilhança , Modelos Genéticos , Análise de Regressão
20.
Mol Ecol Resour ; 13(2): 337-40, 2013 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-23311589

RESUMO

Due to its cost effectiveness, next generation sequencing of pools of individuals (Pool-Seq) is becoming a popular strategy for genome-wide estimation of allele frequencies in population samples. As the allele frequency spectrum provides information about past episodes of selection, Pool-seq is also a promising design for genomic scans for selection. However, no software tool has yet been developed for selection scans based on Pool-Seq data. We introduce Pool-hmm, a Python program for the estimation of allele frequencies and the detection of selective sweeps in a Pool-Seq sample. Pool-hmm includes several options that allow a flexible analysis of Pool-Seq data, and can be run in parallel on several processors. Source code and documentation for Pool-hmm is freely available at https://qgsp.jouy.inra.fr/.


Assuntos
Frequência do Gene , Genômica/instrumentação , Codorniz/genética , Análise de Sequência de DNA/instrumentação , Software , Animais , Sequenciamento de Nucleotídeos em Larga Escala , Internet , Modelos Genéticos , Polimorfismo de Nucleotídeo Único
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