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1.
Genet Sel Evol ; 54(1): 82, 2022 Dec 27.
Artículo en Inglés | MEDLINE | ID: mdl-36575379

RESUMEN

BACKGROUND: The availability of genome-wide marker data allows estimation of inbreeding coefficients (F, the probability of identity-by-descent, IBD) and, in turn, estimation of the rate of inbreeding depression (ΔID). We investigated, by computer simulations, the accuracy of the most popular estimators of inbreeding based on molecular markers when computing F and ΔID in populations under random mating, equalization of parental contributions, and artificially selected populations. We assessed estimators described by Li and Horvitz (FLH1 and FLH2), VanRaden (FVR1 and FVR2), Yang and colleagues (FYA1 and FYA2), marker homozygosity (FHOM), runs of homozygosity (FROH) and estimates based on pedigree (FPED) in comparison with estimates obtained from IBD measures (FIBD). RESULTS: If the allele frequencies of a base population taken as a reference for the computation of inbreeding are known, all estimators based on marker allele frequencies are highly correlated with FIBD and provide accurate estimates of the mean ΔID. If base population allele frequencies are unknown and current frequencies are used in the estimations, the largest correlation with FIBD is generally obtained by FLH1 and the best estimator of ΔID is FYA2. The estimators FVR2 and FLH2 have the poorest performance in most scenarios. The assumption that base population allele frequencies are equal to 0.5 results in very biased estimates of the average inbreeding coefficient but they are highly correlated with FIBD and give relatively good estimates of ΔID. Estimates obtained directly from marker homozygosity (FHOM) substantially overestimated ΔID. Estimates based on runs of homozygosity (FROH) provide accurate estimates of inbreeding and ΔID. Finally, estimates based on pedigree (FPED) show a lower correlation with FIBD than molecular estimators but provide rather accurate estimates of ΔID. An analysis of data from a pig population supports the main findings of the simulations. CONCLUSIONS: When base population allele frequencies are known, all marker-allele frequency-based estimators of inbreeding coefficients generally show a high correlation with FIBD and provide good estimates of ΔID. When base population allele frequencies are unknown, FLH1 is the marker frequency-based estimator that is most correlated with FIBD, and FYA2 provides the most accurate estimates of ΔID. Estimates from FROH are also very precise in most scenarios. The estimators FVR2 and FLH2 have the poorest performances.


Asunto(s)
Depresión Endogámica , Enfermedades Inflamatorias del Intestino , Porcinos , Animales , Endogamia , Polimorfismo de Nucleótido Simple , Homocigoto , Linaje , Genotipo
2.
Genet Sel Evol ; 53(1): 42, 2021 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-33933002

RESUMEN

BACKGROUND: Genomic relationship matrices are used to obtain genomic inbreeding coefficients. However, there are several methodologies to compute these matrices and there is still an unresolved debate on which one provides the best estimate of inbreeding. In this study, we investigated measures of inbreeding obtained from five genomic matrices, including the Nejati-Javaremi allelic relationship matrix (FNEJ), the Li and Horvitz matrix based on excess of homozygosity (FL&H), and the VanRaden (methods 1, FVR1, and 2, FVR2) and Yang (FYAN) genomic relationship matrices. We derived expectations for each inbreeding coefficient, assuming a single locus model, and used these expectations to explain the patterns of the coefficients that were computed from thousands of single nucleotide polymorphism genotypes in a population of Iberian pigs. RESULTS: Except for FNEJ, the evaluated measures of inbreeding do not match with the original definitions of inbreeding coefficient of Wright (correlation) or Malécot (probability). When inbreeding coefficients are interpreted as indicators of variability (heterozygosity) that was gained or lost relative to a base population, both FNEJ and FL&H led to sensible results but this was not the case for FVR1, FVR2 and FYAN. When variability has increased relative to the base, FVR1, FVR2 and FYAN can indicate that it decreased. In fact, based on FYAN, variability is not expected to increase. When variability has decreased, FVR1 and FVR2 can indicate that it has increased. Finally, these three coefficients can indicate that more variability than that present in the base population can be lost, which is also unreasonable. The patterns for these coefficients observed in the pig population were very different, following the derived expectations. As a consequence, the rate of inbreeding depression estimated based on these inbreeding coefficients differed not only in magnitude but also in sign. CONCLUSIONS: Genomic inbreeding coefficients obtained from the diagonal elements of genomic matrices can lead to inconsistent results in terms of gain and loss of genetic variability and inbreeding depression estimates, and thus to misleading interpretations. Although these matrices have proven to be very efficient in increasing the accuracy of genomic predictions, they do not always provide a useful measure of inbreeding.


Asunto(s)
Endogamia/métodos , Modelos Genéticos , Polimorfismo de Nucleótido Simple , Porcinos/genética , Animales
3.
J Anim Breed Genet ; 137(4): 345-355, 2020 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-31713272

RESUMEN

Effective population size is a key parameter in conservation genetics. In the management of conservation programs using pedigree information, there is a consensus that the optimal method for maximizing effective population size is to calculate the contribution of each potential parent (the number of offspring that each individual leaves to the next generation) by minimizing the global pedigree-based coancestry between potential parents weighted by their contributions. When using molecular data, the optimal method for managing genetic diversity will remain the same but now the molecular coancestry calculated from markers will replace the pedigree-based coancestry. However, in this situation, the concept of effective population size loses its meaning because with optimal molecular management, genetic diversity increases in early generations and therefore effective population size takes negative values. Furthermore, in the long term, the molecular effective population size does not attain an asymptotic value but it shows an unpredictable behaviour.


Asunto(s)
Conservación de los Recursos Naturales/métodos , Variación Genética , Modelos Genéticos , Densidad de Población , Animales , Simulación por Computador , Evolución Molecular , Marcadores Genéticos/genética , Endogamia , Linaje
4.
Genet Res (Camb) ; 96: e003, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25022872

RESUMEN

It is well known that the presence of related individuals can affect the inference of population genetic structure from molecular data. This has been verified, for example, on the unsupervised Bayesian clustering algorithm implemented in the software STRUCTURE. This methodology assumes, among others, Hardy-Weinberg and linkage equilibrium within subpopulations. The existence of groups of close relatives, such as full-sib families, may prevent these assumptions to be fulfilled, causing the algorithm to work suboptimally. The purpose of this study was to evaluate the effect of the presence of related individuals on a different methodology (implemented in CLUSTER_DIST) for population genetic structure inference. This approach arranges individuals to maximize the genetic distance between groups and does not make Hardy-Weinberg and linkage equilibrium assumptions. We study the robustness of this approach to the presence of close relatives in a sample using simulated scenarios involving combinations of several factors, including the number of subpopulations, the level of differentiation between them, the number, size and type (full or half-sibs) of families in a sample, and the type and number of molecular markers available for clustering analysis. Results indicate that the methodology that maximizes the genetic distance between subpopulations is less influenced by the presence of related individuals than the program STRUCTURE. Therefore, the former can be used, in combination with the program STRUCTURE, to analyse population genetic structure when related individuals are suspected to be present in a sample.


Asunto(s)
Ligamiento Genético , Estructuras Genéticas , Genética de Población , Algoritmos , Teorema de Bayes , Análisis por Conglomerados , Biología Computacional , Simulación por Computador , Humanos , Modelos Genéticos , Programas Informáticos
5.
J Theor Biol ; 347: 74-83, 2014 Apr 21.
Artículo en Inglés | MEDLINE | ID: mdl-24434740

RESUMEN

In humans, cultural transmission occurs usually by cumulative inheritance, generating complex adaptive behavioral features. Cumulative culture requires key psychological processes (fundamentally imitation and teaching) that are absent or impoverished in non-human primates. In this paper we analyze the role that teaching has played in human cumulative cultural evolution. We assume that a system of cumulative culture generates increasingly adaptive behaviors, that are also more complex and difficult to imitate. Our thesis is that, as cultural traits become more complex, cumulative cultural transmission requires teaching to ensure accurate transmission from one generation to the next. In an increasingly complex cultural environment, we consider that individuals commit errors in imitation. We develop a model of cumulative cultural evolution in a changing environment and show that these errors hamper the process of cultural accumulation. We also show that a system of teaching between parents and offspring that increases the fidelity of imitation unblocks the accumulation and becomes adaptive whenever the gain in fitness compensates the cost of teaching.


Asunto(s)
Evolución Biológica , Cultura , Animales , Modelos Teóricos , Primates/fisiología , Enseñanza
6.
Cureus ; 16(4): e58808, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38784372

RESUMEN

The azygos artery is an uncommon vascular variant of the anterior cerebral artery (ACA). This anomaly is associated in a high percentage with aneurysms. Management of azygos ACA aneurysms represents a surgical challenge. We present five patients who underwent microsurgical treatment for distal azygos ACA aneurysms with complex morphology. Four patients showed subarachnoid hemorrhage (SAH) and one complained of sentinel headache. Early preoperative digital subtraction angiography (DSA) or computerized tomography angiography (CTA) was performed. All patients were treated by surgical clipping via an anterior interhemispheric approach. During follow-up, all patients had a satisfactory outcome, with postoperative angiograms showing complete resolution of aneurysms.

8.
Mol Ecol Resour ; 2023 Mar 12.
Artículo en Inglés | MEDLINE | ID: mdl-36906916

RESUMEN

For both undivided and subdivided populations, the consensus method to maintain genetic diversity is the Optimal Contribution (OC) method. For subdivided populations, this method determines the optimal contribution of each candidate to each subpopulation to maximize global genetic diversity (which implicitly optimizes migration between subpopulations) while balancing the relative levels of coancestry between and within subpopulations. Inbreeding can be controlled by increasing the weight given to within-subpopulation coancestry (λ). Here we extend the original OC method for subdivided populations that used pedigree-based coancestry matrices, to the use of more accurate genomic matrices. Global levels of genetic diversity, measured as expected heterozygosity and allelic diversity, their distributions within and between subpopulations, and the migration pattern between subpopulations, were evaluated via stochastic simulations. The temporal trajectory of allele frequencies was also investigated. The genomic matrices investigated were (i) the matrix based on deviations of the observed number of alleles shared by two individuals from the expected number under Hardy-Weinberg equilibrium; and (ii) a matrix based on a genomic relationship matrix. The matrix based on deviations led to higher global and within-subpopulation expected heterozygosities, lower inbreeding and similar allelic diversity than the second genomic and pedigree-based matrices when a relatively high weight was given to the within-subpopulation coancestries (λ ≥ 5). Under this scenario, allele frequencies moved only slightly away from the initial frequencies. Therefore, the recommended strategy is to use the former matrix in the OC methodology giving a high weight to the within-subpopulation coancestry.

9.
Methods Mol Biol ; 2467: 219-243, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35451778

RESUMEN

The use of genomic information for prediction of future phenotypes or breeding values for the candidates to selection has become a standard over the last decade. However, most procedures for genomic prediction only consider the additive (or substitution) effects associated with polymorphic markers. Nevertheless, the implementation of models that consider nonadditive genetic variation may be interesting because they (1) may increase the ability of prediction, (2) can be used to define mate allocation procedures in plant and animal breeding schemes, and (3) can be used to benefit from nonadditive genetic variation in crossbreeding or purebred breeding schemes. This study reviews the available methods for incorporating nonadditive effects into genomic prediction procedures and their potential applications in predicting future phenotypic performance, mate allocation, and crossbred and purebred selection. Finally, a brief outline of some future research lines is also proposed.


Asunto(s)
Genoma , Modelos Genéticos , Animales , Genómica , Genotipo , Hibridación Genética , Fenotipo , Selección Genética
10.
BMC Genomics ; 12: 473, 2011 Sep 29.
Artículo en Inglés | MEDLINE | ID: mdl-21958071

RESUMEN

BACKGROUND: The turbot (Scophthalmus maximus) is a highly appreciated European aquaculture species. Growth related traits constitute the main goal of the ongoing genetic breeding programs of this species. The recent construction of a consensus linkage map in this species has allowed the selection of a panel of 100 homogeneously distributed markers covering the 26 linkage groups (LG) suitable for QTL search. In this study we addressed the detection of QTL with effect on body weight, length and Fulton's condition factor. RESULTS: Eight families from two genetic breeding programs comprising 814 individuals were used to search for growth related QTL using the panel of microsatellites available for QTL screening. Two different approaches, maximum likelihood and regression interval mapping, were used in order to search for QTL. Up to eleven significant QTL were detected with both methods in at least one family: four for weight on LGs 5, 14, 15 and 16; five for length on LGs 5, 6, 12, 14 and 15; and two for Fulton's condition factor on LGs 3 and 16. In these LGs an association analysis was performed to ascertain the microsatellite marker with the highest apparent effect on the trait, in order to test the possibility of using them for marker assisted selection. CONCLUSIONS: The use of regression interval mapping and maximum likelihood methods for QTL detection provided consistent results in many cases, although the high variation observed for traits mean among families made it difficult to evaluate QTL effects. Finer mapping of detected QTL, looking for tightly linked markers to the causative mutation, and comparative genomics are suggested to deepen in the analysis of QTL in turbot so they can be applied in marker assisted selection programs.


Asunto(s)
Mapeo Cromosómico , Peces Planos/genética , Sitios de Carácter Cuantitativo , Animales , Peso Corporal , Cruzamiento , Peces Planos/crecimiento & desarrollo , Ligamiento Genético , Funciones de Verosimilitud , Repeticiones de Microsatélite , Fenotipo , Análisis de Regresión
11.
BMC Genomics ; 12: 541, 2011 Nov 02.
Artículo en Inglés | MEDLINE | ID: mdl-22047500

RESUMEN

BACKGROUND: Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains used in aquaculture are derived from wild strains that may not have had enough time to adapt to new disease pressures. The turbot is one of the most promising European aquaculture species. Furunculosis, caused by the bacterium Aeromonas salmonicida, produces important losses to turbot industry. An appealing solution is to achieve more robust broodstock, which can prevent or diminish the devastating effects of epizooties. Genomics strategies have been developed in turbot to look for candidate genes for resistance to furunculosis and a genetic map with appropriate density to screen for genomic associations has been also constructed. In the present study, a genome scan for QTL affecting resistance and survival to A. salmonicida in four turbot families was carried out. The objectives were to identify consistent QTL using different statistical approaches (linear regression and maximum likelihood) and to locate the tightest associated markers for their application in genetic breeding strategies. RESULTS: Significant QTL for resistance were identified by the linear regression method in three linkage groups (LGs 4, 6 and 9) and for survival in two LGs (6 and 9). The maximum likelihood methodology identified QTL in three LGs (5, 6 and 9) for both traits. Significant association between disease traits and genotypes was detected for several markers, some of them explaining up to 17% of the phenotypic variance. We also identified candidate genes located in the detected QTL using data from previously mapped markers. CONCLUSIONS: Several regions controlling resistance to A. salmonicida in turbot have been detected. The observed concordance between different statistical methods at particular linkage groups gives consistency to our results. The detected associated markers could be useful for genetic breeding strategies. A finer mapping will be necessary at the detected QTL intervals to narrow associations and around the closely associated markers to look for candidate genes through comparative genomics or positional cloning strategies. The identification of associated variants at specific genes will be essential, together with the QTL associations detected in this study, for future marker assisted selection programs.


Asunto(s)
Aeromonas salmonicida/fisiología , Enfermedades de los Peces/genética , Peces Planos/genética , Forunculosis/veterinaria , Sitios de Carácter Cuantitativo , Animales , Enfermedades de los Peces/microbiología , Forunculosis/genética , Genotipo , Funciones de Verosimilitud , Modelos Lineales , Fenotipo , Análisis de Regresión
12.
PLoS One ; 16(12): e0260729, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34855852

RESUMEN

Intestinal microbiota facilitates food breakdown for energy metabolism and influences the immune response, maintaining mucosal homeostasis. Overall, HIV infection is associated with intestinal dysbiosis and immune activation, which has been related to seroconversion in HIV-exposed individuals. However, it is unclear whether microbiota dysbiosis is the cause or the effect of immune alterations and disease progression or if it could modulate the risk of acquiring the HIV infection. We characterize the intestinal microbiota and determine its association with immune regulation in HIV-exposed seronegative individuals (HESN), HIV-infected progressors (HIV+), and healthy control (HC) subjects. For this, feces and blood were collected. The microbiota composition of HESN showed a significantly higher alpha (p = 0.040) and beta diversity (p = 0.006) compared to HC, but no differences were found compared to HIV+. A lower Treg percentage was observed in HESN (1.77%) than HC (2.98%) and HIV+ (4.02%), with enrichment of the genus Butyrivibrio (p = 0.029) being characteristic of this profile. Moreover, we found that Megasphaera (p = 0.017) and Victivallis (p = 0.0029) also are enriched in the microbiota composition in HESN compared to HC and HIV+ subjects. Interestingly, an increase in Succinivibrio and Prevotella, and a reduction in Bacteroides genus, which is typical of HIV-infected individuals, were observed in both HESN and HIV+, compared to HC. Thus, HESNs have a microbiota profile, similar to that observed in HIV+, most likely because HESN are cohabiting with their HIV+ partners.


Asunto(s)
Microbioma Gastrointestinal , Infecciones por VIH/patología , Adolescente , Adulto , Butyrivibrio/aislamiento & purificación , Estudios de Casos y Controles , Heces/microbiología , Femenino , Infecciones por VIH/inmunología , Seronegatividad para VIH , Humanos , Masculino , Megasphaera/aislamiento & purificación , Persona de Mediana Edad , Prevotella/aislamiento & purificación , Linfocitos T Reguladores/citología , Linfocitos T Reguladores/inmunología , Linfocitos T Reguladores/metabolismo , Células Th17/citología , Células Th17/inmunología , Células Th17/metabolismo , Adulto Joven
13.
BMC Genet ; 11: 76, 2010 Aug 10.
Artículo en Inglés | MEDLINE | ID: mdl-20698974

RESUMEN

BACKGROUND: Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. RESULTS: Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. CONCLUSIONS: During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success.


Asunto(s)
Variación Genética , Genética de Población , Repeticiones de Microsatélite , Oveja Doméstica/genética , Animales , Asia , Teorema de Bayes , Cruzamiento , Análisis por Conglomerados , Europa (Continente) , Fenotipo , Análisis de Secuencia de ADN
14.
Genet Sel Evol ; 42: 33, 2010 Aug 11.
Artículo en Inglés | MEDLINE | ID: mdl-20699012

RESUMEN

Estimation of non-additive genetic effects in animal breeding is important because it increases the accuracy of breeding value prediction and the value of mate allocation procedures. With the advent of genomic selection these ideas should be revisited. The objective of this study was to quantify the efficiency of including dominance effects and practising mating allocation under a whole-genome evaluation scenario. Four strategies of selection, carried out during five generations, were compared by simulation techniques. In the first scenario (MS), individuals were selected based on their own phenotypic information. In the second (GSA), they were selected based on the prediction generated by the Bayes A method of whole-genome evaluation under an additive model. In the third (GSD), the model was expanded to include dominance effects. These three scenarios used random mating to construct future generations, whereas in the fourth one (GSD + MA), matings were optimized by simulated annealing. The advantage of GSD over GSA ranges from 9 to 14% of the expected response and, in addition, using mate allocation (GSD + MA) provides an additional response ranging from 6% to 22%. However, mate selection can improve the expected genetic response over random mating only in the first generation of selection. Furthermore, the efficiency of genomic selection is eroded after a few generations of selection, thus, a continued collection of phenotypic data and re-evaluation will be required.


Asunto(s)
Genoma/genética , Preferencia en el Apareamiento Animal , Selección Genética , Predominio Social , Animales , Genotipo , Desequilibrio de Ligamiento/genética , Filogenia , Polimorfismo de Nucleótido Simple/genética , Sitios de Carácter Cuantitativo/genética
15.
Br J Pharmacol ; 177(22): 5163-5176, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-32888319

RESUMEN

BACKGROUND AND PURPOSE: Peptide P4 was described as a dimerization disruptor of trypanothione reductase (TryR), a homodimeric enzyme essential for survival of trypanosomatids. Determination of the true inhibitory constant (Ki ) for P4 was not achieved because reaction rates continuously decreased with time, even when substrate concentration was kept constant. The aim of this study was to find a suitable kinetic model that could allow characterization of the complex pattern of TryR inhibition caused by P4. EXPERIMENTAL APPROACH: After showing the slow-binding and pseudoirreversible activity of P4 against Leishmania infantum trypanothione reductase (Li-TryR), analysis of the curvatures of the reaction progress curves at different inhibitor concentrations allowed us to define the apparent inhibitory constants (Kiapp ) at five different substrate concentrations. Analysis of the changes in Kiapp values allowed precise definition of the type of inhibition. KEY RESULTS: Li-TryR inhibition by P4 requires two sequential steps that involve rapid generation of a reversible enzyme-inhibitor complex followed by a pseudoirreversible slow inactivation of the enzyme. Recovery of enzyme activity after inhibitor dissociation is barely detectable. P4 is a non-competitive pseudoirreversible inhibitor of Li- TryR that displays an overall inhibition constant (Ki* ) smaller than 0.02 µM. CONCLUSION AND IMPLICATIONS: Li-TryRdimer disruption by peptide P4 is a pseudoirreversible time-dependent process which is non-competitive with respect to the oxidized trypanothione (TS2 ) substrate. Therefore, unlike reversible Li-TryR competitive inhibitors, enzyme inhibition by P4 is not affected by the TS2 accumulation observed during oxidant processes such as the oxidative burst in host macrophages.


Asunto(s)
Leishmania infantum , NADH NADPH Oxidorreductasas , Dimerización , Inhibidores Enzimáticos/farmacología , Leishmania infantum/metabolismo , NADH NADPH Oxidorreductasas/metabolismo
16.
Genet Sel Evol ; 41: 49, 2009 Nov 09.
Artículo en Inglés | MEDLINE | ID: mdl-19900278

RESUMEN

BACKGROUND: The inference of the hidden structure of a population is an essential issue in population genetics. Recently, several methods have been proposed to infer population structure in population genetics. METHODS: In this study, a new method to infer the number of clusters and to assign individuals to the inferred populations is proposed. This approach does not make any assumption on Hardy-Weinberg and linkage equilibrium. The implemented criterion is the maximisation (via a simulated annealing algorithm) of the averaged genetic distance between a predefined number of clusters. The performance of this method is compared with two Bayesian approaches: STRUCTURE and BAPS, using simulated data and also a real human data set. RESULTS: The simulations show that with a reduced number of markers, BAPS overestimates the number of clusters and presents a reduced proportion of correct groupings. The accuracy of the new method is approximately the same as for STRUCTURE. Also, in Hardy-Weinberg and linkage disequilibrium cases, BAPS performs incorrectly. In these situations, STRUCTURE and the new method show an equivalent behaviour with respect to the number of inferred clusters, although the proportion of correct groupings is slightly better with the new method. Re-establishing equilibrium with the randomisation procedures improves the precision of the Bayesian approaches. All methods have a good precision for F(ST) >or= 0.03, but only STRUCTURE estimates the correct number of clusters for F(ST) as low as 0.01. In situations with a high number of clusters or a more complex population structure, MGD performs better than STRUCTURE and BAPS. The results for a human data set analysed with the new method are congruent with the geographical regions previously found. CONCLUSION: This new method used to infer the hidden structure in a population, based on the maximisation of the genetic distance and not taking into consideration any assumption about Hardy-Weinberg and linkage equilibrium, performs well under different simulated scenarios and with real data. Therefore, it could be a useful tool to determine genetically homogeneous groups, especially in those situations where the number of clusters is high, with complex population structure and where Hardy-Weinberg and/or linkage equilibrium are present.


Asunto(s)
Ligamiento Genético , Estructuras Genéticas , Genética de Población/métodos , Algoritmos , Humanos , Modelos Genéticos , Programas Informáticos
17.
Theor Popul Biol ; 74(1): 1-5, 2008 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-18490041

RESUMEN

Cooperation among genetically unrelated individuals can arise when pairs of individuals interact repeatedly in the Prisoner's Dilemma. However, the conditions allowing the evolution of reciprocal cooperation become extremely restrictive as the size of the cooperative group increases, because defectors can exploit cooperators more efficiently in larger groups. Here we consider three strategies: Tit for Tat, defector, and loner. Loner beats defector in a non-cooperative world. However, a cooperative strategy Tit for Tat (TFT(0)) that stops cooperation after the first iteration when there is at least one defector in the group, can invade a world of loners, even in sizable groups, if both the TFT(0) and the defector strategies arise at the same frequency by mutation.


Asunto(s)
Conducta Cooperativa , Procesos de Grupo , Modelos Teóricos , Humanos , Modelos Estadísticos
18.
Conserv Biol ; 22(5): 1277-87, 2008 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-18680505

RESUMEN

Optimization of contributions of parents to progeny by minimizing the average coancestry of the progeny is an effective strategy for maintaining genetic diversity in ex situ conservation programs, but its application on the basis of molecular markers has the negative collateral effect of homogenizing the allelic frequencies at each locus. Because one of the objectives of a conservation program is to preserve the genetic composition of the original endangered population, we devised a method in which markers are used to maintain the allele frequency distribution at each locus as closely as possible to that of the native population. Contributions of parents were obtained so as to minimize changes in allele frequency for a set of molecular markers in a population of reduced size. We used computer simulations, under a range of scenarios, to assess the effectiveness of the method in comparison with methods in which contributions of minimum coancestry are sought, either making use of molecular markers or genealogical information. Our simulations indicated that the proposed method effectively maintained the original distribution of allele frequencies, particularly under strong linkage, and maintained acceptable levels of genetic diversity in the population. Nevertheless, contributions of minimum coancestry determined from pedigree information but ignoring the genealogy previous to the conservation program, was the most effective method for maintaining allelic frequencies in realistic situations.


Asunto(s)
Conservación de los Recursos Naturales/métodos , Variación Genética , Genética de Población , Modelos Genéticos , Simulación por Computador , Frecuencia de los Genes , Marcadores Genéticos
19.
Front Genet ; 9: 78, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29559995

RESUMEN

In the last decade, genomic selection has become a standard in the genetic evaluation of livestock populations. However, most procedures for the implementation of genomic selection only consider the additive effects associated with SNP (Single Nucleotide Polymorphism) markers used to calculate the prediction of the breeding values of candidates for selection. Nevertheless, the availability of estimates of non-additive effects is of interest because: (i) they contribute to an increase in the accuracy of the prediction of breeding values and the genetic response; (ii) they allow the definition of mate allocation procedures between candidates for selection; and (iii) they can be used to enhance non-additive genetic variation through the definition of appropriate crossbreeding or purebred breeding schemes. This study presents a review of methods for the incorporation of non-additive genetic effects into genomic selection procedures and their potential applications in the prediction of future performance, mate allocation, crossbreeding, and purebred selection. The work concludes with a brief outline of some ideas for future lines of that may help the standard inclusion of non-additive effects in genomic selection.

20.
Eur J Med Chem ; 149: 238-247, 2018 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-29501944

RESUMEN

Trypanothione reductase (TryR) is a well-established target in the search for novel antitrypanosomal and antileishmanial agents. We have previously identified linear and lactam-bridged 13-residue peptides derived from an α-helical region making up part of the dimeric interface of Leishmania infantum TryR (Li-TryR) which prevent trypanothione reduction by disrupting enzyme dimerization. We now show that i,i + 4 side-chain cross-linking with an all-hydrocarbon staple stabilizes the helical structure of these peptides and significantly improves their resistance to protease cleavage relative to previous linear and cyclic lactam analogues. Interestingly, replacement of the amide bridge by the hydrocarbon staple at the same cyclization positions generates derivatives (2 and 3) that similarly inhibit oxidoreductase activity of the enzyme but unexpectedly stabilize the TryR homodimer. The most proteolytically stable peptide 2 covalently linked to oligoarginines displayed potent in vitro leishmanicidal activity against L. infantum parasites.


Asunto(s)
Antiprotozoarios/química , NADH NADPH Oxidorreductasas/antagonistas & inhibidores , Péptidos/farmacología , Estabilidad de Medicamentos , Hidrocarburos/química , Leishmania infantum/efectos de los fármacos , Péptidos/química , Conformación Proteica en Hélice alfa , Proteolisis , Proteínas Protozoarias/antagonistas & inhibidores
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