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Twenty nuclear DNA polymorphisms in a Moroccan population: a comparison with seven other human populations

Twenty nuclear DNA polymorphisms in a Moroccan population: a comparison with seven other human populations

ropean and sub-Saharan African groups, Reynolds’ genetic distance coefficients were calculated (data not shown) and represented in a neighbor-joining tree (Fig- ure 2). Distance estimates indicate that the closest populations to Morocco were La Alpujarra (0.041 ± 0.01) and Basques (0.043 ± 0.02), followed by Italians (0.045 ± 0.02). Average distance between sub-Saharan populations and Morocco was 0.155 ± 0.01, almost four times greater than the mean distance between the European groups and Morocco (0.046 ± 0.00). In general, lowest genetic dis- tances corresponded to intra-European comparisons (average: 0.015); genetic dis- tances among Africans were remarkably higher (average: 0.076), whereas the highest values corresponding to those between groups of the two continents (0.169). Consistently, the neighbor-joining tree in Figure 2 displayed two main population clusters: sub-Saharan Africa and the rest. The inclusion of Morocco within the European group reflects that genetic relationships closely matched geographical relationships. However, inside this group Morocco appears as the most differentiated population, a differentiation with a strong bootstrap support after 1000 iterations (85%). Among Europeans, the Mediterranean populations exhibited short branch-lengths, as is particularly evident for the two Spanish groups included in the comparison.

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Anlisis de polimorfismo gentico en especies salvajes de Nicotiana y tabaco cultivado en Cuba mediante AFLP

Anlisis de polimorfismo gentico en especies salvajes de Nicotiana y tabaco cultivado en Cuba mediante AFLP

ABSTRACT Wild Nicotiana species are commonly used in tobacco’s breeding programs to obtain cultivars of enhanced pro- ductivity, and to improve its tolerance or resistance to diseases or different types of stress. In Cuba, tobacco pro- duction is one of the main sources of economic income and during the last decades several new tobacco varieties have been generated, being essential to study their genetic background for better crop management. In this work, the genetic polymorphism of four Cuban varieties of Nicotiana tabacum L. and six wild species used in Cuban tobacco breeding programs were assessed through AFLP analysis. Polymorphic profiles were obtained with four selective primers combinations (EcoR I/Mse I) among the studied accessions. A total of 203 polymorphic bands (57.79 %) were used for cluster analysis (UPGMA) based on genetic similarity and genetic distance matrices. A common group was detected, comprising all the cultivated varieties that showed high genetic similarity (0.87446- 0.93920) according to the Nei and Li’s distance measure, whereas wild species showed the highest genetic di- versity. It was also possible to identify some bands shared among cultivated accession as specific markers for the analyzed Cuban cultivated tobacco. Our results indicate that AFLP analysis effectively detects the genetic diversity at levels enough to differentiate wild species of Nicotiana from Cuban varieties of N. tabacum, even though a nar- row genetic diversity was present in Cuban varieties. All the accessions were distinguished through AFLP analysis.

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Appendix 1 – Methods and Statistics in GenAlEx 6.1 By Rod Peakall and Peter Smouse

Appendix 1 – Methods and Statistics in GenAlEx 6.1 By Rod Peakall and Peter Smouse

This Codom-Microsat distance option produces a 2N x 2N distance matrix. The first allele of individual 1 is presented, followed by the second allele of individual 1, then the first allele of individual 2, and so on. Alleles must be coded by size, either the inferred number of repeats or the size of the allele in base pairs (bp). The genetic distance is calculated as the sum of the squared size difference between the two alleles in the comparisons: (S1 – S2) 2 , where S1 is the size of allele 1 and S2 the size of allele 2. Distances are summed across loci. This genetic distance option can only be generated when GenAlEx is calculating Rst via AMOVA. Rst is an estimator of genetic differentiation for microsatellite loci that assumes a stepwise mutation model [12, 19]. It is not necessary to output this distance matrix for the AMOVA analysis, and since this matrix cannot be used for other analyses, its output is not generally recommended, except for advanced users. See AMOVA above, and Rst in Table 2.

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Variación genética de Pinus pinceana Gordon evidencia de conectividad en poblaciones fragmentadas

Variación genética de Pinus pinceana Gordon evidencia de conectividad en poblaciones fragmentadas

The genetic distance (Jaccard) was calculated based on the binary matrix and was subsequently subjected to a Principal Coordinates (PCO) analysis using the PAST software, version 3 (Hammer et al. 2001), which produces a visual representation of the genetic relationship within and between the populations. Furthermore, a dendrogram was built using the UPGMA (Unweighted Pair Group Method with Arithmetic averages) method based on the genetic distance between pairs of populations. The bootstrap analysis was carried out with 1 000 repetitions. The FAMD (Fingerprint Analysis with Missing Data) software, version 1.25, was used for both analyses (Schlüter and Harris, 2006).

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Abstract: In Mexico and elsewhere in the Caribbean, the queen conch Strombus gigas is an endangered spe- cies. Understanding the genetic connectivity of their populations will support management strategies for long term conservation of the species. Genetic diversity and population differentiation was assessed from samples collected at Banco Chinchorro and Isla Cozumel in the Mexican Caribbean and at Arrecife Alacranes in the Gulf of Mexico. Samples were obtained from the commercial capture at Banco Chinchorro (n=50) and Isla Cozumel (n=40) on March 2004. On November 2004, a non-invasive method for the Arrecife Alacranes sampling was applied, taking the hemolymph of live animals (n=65) and releasing them to the wild. The mitochondrial DNA variation at two genes (COI and Cyt-b) was analyzed. Genetic diversity at the three locations ranged between 0.55-0.65 in COI and 0.87-0.94 in Cyt-b, showing no bottleneck evidences. A non-significant fixation index (F ST =0.019, p=0.161) and a Maximum Parsimony Network tree that did not show particular clades associated with any of the geographical locations, suggested a lack of statistically significant genetic differentiation among populations. Nevertheless, the cline patterns observed in both genetic diversity and haplotypic frequencies from Banco Chinchorro through Arrecife Alacranes, and the larger genetic distance between these locations from those between Isla Cozumel, Banco Chinchorro and Arrecife Alacranes, suggest the possibility of a pattern of isolation-by distance. The role of the main current systems over the potential genetic differences in S. gigas populations along the Mexican Caribbean, and the conservation management of S. gigas at these locations as discrete units is discussed. Rev. Biol. Trop. 59 (3): 1115-1126. Epub 2011 September 01.

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Plasmodium vivax lineages: geographical distribution, tandem repeat polymorphism, and phylogenetic relationship

Plasmodium vivax lineages: geographical distribution, tandem repeat polymorphism, and phylogenetic relationship

subdivision, as both lineages may have attained geographi- cal sympatricity due to a gene flow mechanism. Their genetic relatedness was characterized by using 48 S type-1 and 48 S type-2 lineage samples to rule this out. The genetic relatedness analysis showed that both proposed genetic lineages were from the same P. vivax population based on the lack of genetic distance, similar genetic diver- sity magnitude, and no separate phylogenetic clade/cluster. As per Li et al., it was assumed that S type-2 lineage (New World) is a recently evolved species and it was expected that S type-2 lineage would be less diverse, and form a separate phylogenetic clade, if the hypothesis was correct. However, the panel of genomic markers consistently revealed similar patterns with all parameters used, provid- ing no support for the hypothesis that S type-2 lineage is a subspecies of P. vivax. This clearly suggested that S type 18S SSU rRNA gene polymorphism (S type-1 and S type-2) Table 2 Regional distribution of S type-1 and S type-2 lineages and malaria vector prevalence

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Variabilidad genética en germoplasma argentino de manzano silvestre (Malus spp)

Variabilidad genética en germoplasma argentino de manzano silvestre (Malus spp)

Kyndt, T.; Assogbadjo, A.E.; Hardy, Olivier J.; Glele Kakaï, R.; Sinsin, B.; Van Damme, P; Gheysen, G. 2009. Spatial genetic structuring of baobab (Adansonia digitata L., Malvaceae) in the traditional agroforestry systems of West Africa. American Journal of Botany, 96(5): 950-957.

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The autonomous learning strategies for distance education.

The autonomous learning strategies for distance education.

For Garcia Arieto L. (2003), the other sector that can be benefited by the distance education system is the governments. For the author these sectors have the possibility to: “a) offer to the citizenship more opportunities for the permanent formation, recycling, cultural promotion, and the personal enrichment. b) reduce the education costs. c) diversify the educative offers, raise and consolidate the permanent training” (p, 15). According to this, governments can reduce some costs related to the educative programs, this is because of the fact that they do not have to invest more economic resources, in the building of huge infrastructures, besides the design of academic programs that allow the citizens to be prepared to face the several social challenges.

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Geometric quantum discord with Bures distance

Geometric quantum discord with Bures distance

Abstract. We define a new measure of quantum correlations in bipartite quantum systems given by the Bures distance of the system state to the set of classical states with respect to one subsystem, that is, to the states with zero quantum discord. Our measure is a geometrical version of the quantum discord. As the latter it quantifies the degree of non-classicality in the system. For pure states it is identical to the geometric measure of entanglement. We show that for mixed states it coincides with the optimal success probability of an ambiguous quantum state discrimination task. Moreover, the closest zero-discord states to a state ρ are obtained in terms of the corresponding optimal measurements.

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Estructura genética poblacional de diversas especies de Ascidias (Tunicata, Ascidiacea) en dos sistemas polares: Islas Shetland del Sur (Antártida) y Kongsfjord, Spitsbergen (Ártico).

Estructura genética poblacional de diversas especies de Ascidias (Tunicata, Ascidiacea) en dos sistemas polares: Islas Shetland del Sur (Antártida) y Kongsfjord, Spitsbergen (Ártico).

more gene X ow between them than between the more dis- tant ones. The cluster analysis also highlighted the potential gene Xow among the South Shetland Islands populations, as individuals from Low1, Low2 and Liv were clustered together. SOI and SGI were grouped as separate branches, with SOI being closer to South Shetland Island populations than to SGI. A strong genetic structuring was also found in other species of colonial ascidians such as Pseudodistoma crucigaster from southwestern Mediterranean (Tarjuelo et al. 2004), Botryllus schlosseri from New Zealand (Ben- Shlomo et al. 2001), and from Maine, USA, in a microgeo- graphic scale (Yund and O’Neil 2000). Additionally, there is evidence of restricted gene X ow in other species of Antarctic marine organisms. In an allozyme survey of the Antarctic limpet Nacella concinna, diVerences in allele fre- quency were detected between populations located in South Georgia and in South Orkney Island (Beaumont and Wei 1991). Wilson et al. (2007) reported restricted gene Xow in the crinoid Promachocrinus kerguelensis of the Antarctic Peninsula, South Sandwich Is., South Georgia and Bou- vetøya Islands, a surprising W nd because of the presence of the ACC which assist in directing water from one popula- tion to the other. Brierley et al. (1993) found absence of panmixia in populations of the squid Martialia hyadesi

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MODELING AUDITORY DISTANCE PERCEPTION IN ROOMS

MODELING AUDITORY DISTANCE PERCEPTION IN ROOMS

The D/R ratio is a particularly interesting cue because it is, in principle, absolute (i.e., independent of source intensity) and able to code a wide range of distances in many different enclosed or semi-enclosed environments. The cue is also of interest because it has apparent limitations. It has been shown repeatedly that the perceived distance of a sound source in a room is compressed: it increases virtually linearly with source distance at short range, but converges to a certain limit when the source distance is increased further [6-9]. This limit acts as a sort of “auditory horizon”, which is, however, not constant but depends on the acoustic environment. Another intriguing finding about the D/R ratio is that direct measurement of its just noticeable difference yield values in the order of 6 dB, which translate to unexpectedly large differences in distance [11]. This result seems to suggest that the D/R ratio cue provides distance coding that is coarser than the resolution found in distance perception experiments. However, it is not clear which other cues could have been used instead, particularly in experiments designed to eliminate or minimise cues based on intensity and interaural differences.

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Minimal distance from a point to n lines

Minimal distance from a point to n lines

We present a solution to the problem of computing a point in the plane minimizing the distance to n given lines. We used an experimental mathematics approach: using dynamic geometry software, we gathered data which allowed us to conjecture and testing our hypothesis. Finally we formalized our reasoning to prove the conjecture. Although this solution was known, our method could be of interest.

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e-learning for expanding distance education in tertiary level in Bangladesh: Problems and progress

e-learning for expanding distance education in tertiary level in Bangladesh: Problems and progress

The mode of teaching is very significant for distance learning. Mixed approach uses several different media methods or deliveries, such as video and e-mail, compared to single mode which is one delivery method in BOU. According to Hirsch Buhl, Jackson, and Bishop (1995), “...single mode delivery systems do not provide enough instructional power to ignite the student’s interest because they fail to provide student involvement”. As a distinct mode of imparting education, BOU relies heavily on print materials, electronic media like radio- television and audio-video cassettes, and face-to-face tutorial services. The use of these techniques helps BOU to take its academic programs to the doorsteps of people far and wide. It makes room for in-house education. Considering the rapid expansion of ICTs in the country, BOU should introduce more electronic media like CD-ROM, e-mail, and internet for its advanced learners (Table1). Indeed, BOU has been broadcasting some radio and TV programs for the students of each formal program through national TV and radio. The broadcasting time of those programs are sometimes not convenient to the target learners. In such a situation, efforts are underway to introduce video conferencing and web-based materials for distance delivery in BOU. It is also important to mention that BOU is now supplying audio and video materials as supplementary component to most of the programs (Hossain & EI Saddik, 2003; see also Kamal & Sultana, 2002). So, BOU could easily create copies of those recorded programs on multimedia CDs and add with respective pack up of course materials (Table 1).

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Genetic, genomic and epigenetic alterations in congenital malformations : implications in genetic counseling

Genetic, genomic and epigenetic alterations in congenital malformations : implications in genetic counseling

Subsequently, an unbiased approach for the entire cohort was considered to analyze the results regardless to the gene function. With this aim, only private variants were considered (not described in dbSNP or in the Nijmegen in-house database). An overlap analysis was performed in order to identify genes with a possible mutation in several samples (10). We prioritized the genes with variants in three or more samples and also some genes with a variant in two samples if both variants showed a high PhyloP (basepair conservation) value (phyloP > 5.0). For the overlap analysis, data from a cohort of the same sample size but resenting a different phenotype was used to exclude an enrichment of genes displaying an excess of genetic variation. The list of genes obtained in the overlap analysis was compared to the genes with variants in a cohort of 14 samples of patients with congenital heart defects (CHD). By using the same list of private variants, a second analysis was done regarding the most damaging variants, nonsense as well as frameshift. Among those variants, only the ones in genes with no nonsense variants described in Exome Variant Server (EVS) (11) were selected for further studies. The availability of parental samples was also considered for validations. For the third approach, a candidate gene list consisting of 390 genes (supplementary table 2) for neural tube defects was elaborated including genes previously described in humans related to a similar type of disease, as

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TítuloPopulation genetic analysis and characterization of nuclear gene regions and mitogenomes in four European "Donax" species

TítuloPopulation genetic analysis and characterization of nuclear gene regions and mitogenomes in four European "Donax" species

Quesada et al., 1995; Sanjuan et al., 1996, 1997; Diz and Presa, 2008; Luis et al., 2011) and in the scallops Pecten jacobaeus and Pecten maximus (Ríos et al., 2002), or in other marine organisms such as Dicentrarchus labrax (Naciri et al., 1999), Meganyctiphanes norvegica (Zane et al., 2000), Serranus cabrilla (Schunter et al., 2011) or Liocarcinus depurator (García-Merchán et al., 2012). The Alboran Sea, located west of the Mediterranean Sea, borders the Atlantic Ocean along the Strait of Gibraltar. This region is a transition zone between two basins with different oceanographic characteristics where Atlantic and Mediterranean species coexist. The Almeria- Oran front is an area of strong currents where abrupt temperature and salinity changes occur (Tintore et al., 1988). This area constitutes an oceanographic barrier to dispersal of planktonic larvae and therefore can prevent gene flow between the Atlantic and Mediterranean populations, thereby contributing to their differentiation. The location of FU, within the Alboran Sea and limited in the east by the Almeria-Oran front and in the west by the Strait of Gibraltar, could contribute to the observed genetic differentiation. In addition, the differentiation between localities on both sides of the Almeria-Oran front and between FU and localities from the Atlantic Ocean, is reinforced by previous results obtained with samples from FU or its vicinity (Marie et al., 2016; Nantón et al., 2017), which also indicated the existence of biogeographical barriers to gene flow of D. trunculus in this area.

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Analysis and optimization of composite stringers

Analysis and optimization of composite stringers

A structure of special interest which has been the object of optimization routines are composite panels stiffened with stringers. The optimization of the set panel-stringer is of high interest since this kind of structure is widely used in the aircraft industry. For them, Genetic Algorithms (GAs) [7], a family of evolutionary algorithms, have been succesfully used, as reported in a large number of publications [8–12] among others. A case of special interest reported in the scientific literature is the optimization of the stacking sequence of composite laminates, for which GA have been used successfully [13, 14]. However, in situations where the stacking sequence cannot be considered as a design variable but a imposed requirement, the minimization of the weight is achieved with geometrical parameters [15, 16]. In that case, what makes different the optimization of composite structures from other materials is the use of failure mode based failure criteria such as Puck’s [17] and LaRC [18]. These are in fact a set of failure criteria which assign a different index for the different failure modes under consideration. When they are included in optimization routines as non-smooth discontinuous constraints, the resulting optimization problem is very specific of composite materials, as can be concluded from some works analysing the effect of different failure criteria in the optimal solution [19–21].

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Distance and overcurrent relay coordination considering non standardized inverse time curves

Distance and overcurrent relay coordination considering non standardized inverse time curves

Suppose a rough example where wireless sensors have to be automatically deployed in a mountain — as illustrated in Figure 2.22 — with the aim of conform a network and report hazardous situations by communicating the compiled environmental information. The position of the sensors and the distance between them are used by the objective func- tion. Considering a four chromosomes population, the supposed fitness results of each one are displayed in the second column of Table 2.5 and the roulette portion assigned by the fitness-based option on the third. There might be generations — specially the initial ones — where the fittest element is much better than the others, on this example the best ele- ment would cover the 70% of the roulette-wheel. This situation may cause the population of selected parents to be dominated by this element, reducing the diversity and increasing the possibility of premature convergence.

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Relación entre la estructura genética del sapo andino Rhinella spinulosa (Anura: Bufonidae) y el paisaje del norte de Chile (21°  24° S)

Relación entre la estructura genética del sapo andino Rhinella spinulosa (Anura: Bufonidae) y el paisaje del norte de Chile (21° 24° S)

The group analyzed using the results of SAMOVA showed that annual precipitation explained the genetic dif fer entiation, in agreement with the analysis of all populations. However, the wetland-based route was selected instead of the Euclidean distance. We suggest that the wetland-based route is related to a recent diversifi cation pattern, as is shown by localities with little genetic dif ferentiation. This patter n was also detected by Cor rea et al. (2010), suggesting that it could be related to an early divergence among these populations. The wetland-based route is based on a stepping stone model. This pattern may be related to changes in the precipitation regime in the Altiplano zone, which have had ef fects on the expansion and contraction of the vegetation since the end of the Pleistocene and during all of the Holocene (Betancourt et al. 2000, Latorre et al. 2006, Quade et al. 2008). Wetlands are the only appropriate habitat for R. spinulosa; the desert is much more hostile for this species. For this reason, we expected this route to be selected in our model, because the ability of amphibians to move between isolated populations is largely dependent on the suitability of habitat among populations (Marsh et al. 2001).

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Seeholzer et al 2018 Isolation by distance, not incipient ecological speciation, explains genetic pdf

Seeholzer et al 2018 Isolation by distance, not incipient ecological speciation, explains genetic pdf

Plumage and vocal differences are expected to play a more impor- tant role in conspecific recognition and mate-choice in birds than body size (Price, 2007) and thus may be important in structuring genetic variation. We found little support for the role of selection in shaping plumage variation, and plumage divergence explained almost none of the variation in genetic divergence in our dataset (Table 3, Figure 5). We also examined preliminary data on song. These data indicate that the peak frequency of the song of C. antisiensis (a stac- cato series of accelerating, descending notes) is negatively correlated with cline position, elevation, and temperature (GFS unpublished data). Although we do not have body mass associated with the vocal data, it is clear that larger birds in the south have lower peak fre- quencies than smaller birds in the north, as predicted by the scaling of the syrinx with body size (Ryan & Brenowitz, 1985). Thus, natural selection may be indirectly driving song divergence through its influ- ence on body size variation (Podos, 2001). This hypothesis could be tested by resampling the transect to obtain recordings for vouchered specimens with body mass data. Still, due to the expected co-linear- ity of song variation with body mass, we doubt song divergence will exceed the strength of IBD.

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Sofía Solórzano , Patricia Diana Cuevas-Alducin, Verónica García-Gómez and Patricia Dávila

Sofía Solórzano , Patricia Diana Cuevas-Alducin, Verónica García-Gómez and Patricia Dávila

In plants, the geographical distribution, population size, pollination system and seed dispersion are the main factors that determine the levels of genetic diversity within and among populations (e.g., Ellstrand, 1992; Ellstrand and Elam, 1993; Nassar et al., 2001). These processes and factors do not have to act in conjunction to have a significant impact on the genetic properties of populations. For example, pollination performed by generalist insects promotes high genetic differentiation (Kramer et al., 2011; Magalhaes et al., 2011), whereas plants that are pollinated by wind or vertebrates tend to be genetically homogenous (Ellstrand, 1992; Nassar et al., 2001), irrespective of the geographical distribution pattern of the populations. In contrast, small population size combined with a narrow distribution range has been associated with low levels of genetic diversity (cf. Purdy and Bayer, 1996; Dodd and Helenurm, 2002; Gibson et al., 2008) and with high intraspecific genetic differentiation promoted by genetic drift (Frankham et al., 2002).

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