Genetica

Erratum to: Multilocus phylogeography and phylogenetics using sequence-based markers.

Publication Date: 2010 Mar 4 PMID: 20204466
Authors: Brito, P. H. - Edwards, S. V.
Journal: Genetica

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Erratum to: Gene mapping in the wild with SNPs: guidelines and future directions.

Publication Date: 2010 Mar 4 PMID: 20204465
Authors: Slate, J. - Gratten, J. - Beraldi, D. - Stapley, J. - Hale, M. - Pemberton, J. M.
Journal: Genetica

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Erratum to: Search for informative polymorphisms in candidate genes: clock genes and circadian behaviour in blue tits.

Publication Date: 2010 Mar 5 PMID: 20204464
Authors: Steinmeyer, C. - Mueller, J. C. - Kempenaers, B.
Journal: Genetica

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Erratum to: Ecological genomics and conservation: where do we stand?

Publication Date: 2010 Mar 4 PMID: 20204463
Authors: Segelbacher, G. - Hoglund, J.
Journal: Genetica

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Erratum to: Evolutionary history of Na,K-ATPases and their osmoregulatory role.

Publication Date: 2010 Mar 4 PMID: 20204462
Authors: Saez, A. G. - Lozano, E. - Zaldivar-Riveron, A.
Journal: Genetica

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Are large wattles related to particular MHC genotypes in the male pheasant?

Publication Date: 2010 Feb 10 PMID: 20145977
Authors: Baratti, M. - Ammannati, M. - Magnelli, C. - Massolo, A. - Dessi-Fulgheri, F.
Journal: Genetica

In sexually dimorphic species, partners can assess heritable mate quality by analyzing costly sexual ornaments in terms of their dimension and possibly of their symmetry. In vertebrates an important aspect of genetic quality is the efficiency of the immune system, and in particular the Major Histocompatibility Complex (MHC). If ornaments are honest advertisements of pathogen resistance (good genes), in line with the Hamilton-Zuk hypothesis, a correlation between ornament expression and MHC profiles should exist. We tested this hypothesis in the common pheasant Phasianus colchicus by comparing male ornament characteristics (wattle and spur size, and wattle fluctuating asymmetry) with a portion of exon 2 of the class IIB MHC genes containing 19 putative antigen recognition sites. A total of 8 new alleles was observed in the MHCPhco exon IIB. We found significant differences in the occurrence of MHC genotypes between males carrying large or small wattles. Homozygous genotypes predicted large wattle males more correctly than small wattle males. The association between the dimension of the spur and the occurrence of MHC genotypes was marginally significant, however, we did not find any significant association between MHC genotypes and asymmetry. Our results suggest that female pheasants may use the ornament size as a cue to evaluate male quality and thus choose males carrying particular MHC profiles.

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Genetic divergence among sympatric colour morphs of the Dalmatian wall lizard (Podarcis melisellensis).

Publication Date: 2010 Mar PMID: 20128114
Authors: Huyghe, K. - Small, M. - Vanhooydonck, B. - Herrel, A. - Tadic, Z. - Van Damme, R. - Backeljau, T.
Journal: Genetica

If alternative phenotypes in polymorphic populations do not mate randomly, they can be used as model systems to study adaptive diversification and possibly the early stages of sympatric speciation. In this case, non random mating is expected to support genetic divergence among the different phenotypes. In the present study, we use population genetic analyses to test putatively neutral genetic divergence (of microsatellite loci) among three colour morphs of the lizard Podarcis melisellensis, which is associated with differences in male morphology, performance and behaviour. We found weak evidence of genetic divergence, indicating that gene flow is somewhat restricted among morphs and suggesting possible adaptive diversification.

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Geographic and molecular variation in a natural plant transgene.

Publication Date: 2010 Mar PMID: 20128113
Authors: Vallenback, P. - Bengtsson, B. O. - Ghatnekar, L.
Journal: Genetica

A PCR based survey of Festuca ovina plants from populations around the southern part of the Baltic Sea demonstrates both geographic and molecular variation in the enzyme gene PgiC2, horizontally transferred from a Poa-species. Our results show that PgiC2-a natural functional nuclear transgene-is not a local ephemeral phenomenon but is present in a very large number of individuals. We find also that its frequency is geographically variable and that it appears in more than one molecular form. The chloroplast variation in the region does not indicate any distinct subdivision due to different colonization routes after the last glaciation. Our data illustrate the geographic and molecular variation that may occur in natural populations with a polymorphic, unfixed transgene affected by diverse kinds of mutational and evolutionary processes.

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Bayesian model averaging for evaluation of candidate gene effects.

Publication Date: 2010 Mar PMID: 20049510
Authors: Wu, X. L. - Gianola, D. - Rosa, G. J. - Weigel, K. A.
Journal: Genetica

Statistical assessment of candidate gene effects can be viewed as a problem of variable selection and model comparison. Given a certain number of genes to be considered, many possible models may fit to the data well, each including a specific set of gene effects and possibly their interactions. The question arises as to which of these models is most plausible. Inference about candidate gene effects based on a specific model ignores uncertainty about model choice. Here, a Bayesian model averaging approach is proposed for evaluation of candidate gene effects. The method is implemented through simultaneous sampling of multiple models. By averaging over a set of competing models, the Bayesian model averaging approach incorporates model uncertainty into inferences about candidate gene effects. Features of the method are demonstrated using a simulated data set with ten candidate genes under consideration.

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Population genetic structure of the oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) from Yunnan province (China) and nearby sites across the border.

Publication Date: 2010 Mar PMID: 20012674
Authors: Shi, W. - Kerdelhue, C. - Ye, H.
Journal: Genetica

Bactrocera dorsalis (Diptera: Tephritidae) is an important pest for many tropical and subtropical fruits. The fly is probably introduced in Yunnan, a southwestern province of China that shares borders with Vietnam, Laos and Myanmar. Depending on local environmental conditions, this species occurs either only in the most favorable seasons or year-round. To infer the genetic diversity and structure of the fly in the region, and to understand the relationships between the flies of year-round and seasonal areas, we analyzed 304 individuals from 14 populations using the mitochondrial cytochrome oxidase I gene (COI). The sampled populations were structured into four groups, probably isolated by the main natural barriers in Yunnan such as mountain ranges and rivers. Our data suggest either that B. dorsalis in Yunnan originated from multiple introductions events, even if the source populations still need to be identified; or that Yunnan is a natural origin of this species (i.e., that it is not invasive there). Finally, we found some evidences that the seasonal populations were colonized from nearby year-round populations.

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Transposon tools: worldwide landscape of intellectual property and technological developments.

Publication Date: 2010 Mar PMID: 19957019
Authors: Palazzoli, F. - Testu, F. X. - Merly, F. - Bigot, Y.
Journal: Genetica

DNA transposons are considered to be good candidates for developing tools for genome engineering, insertional mutagenesis and gene delivery for therapeutic purposes, as illustrated by the recent first clinical trial of a transposon. In this article we set out to highlight the interest of patent information, and to develop a strategy for the technological development of transposon tools, similar to what has been done in many other fields. We propose a patent landscape for transposon tools, including the changes in international patent applications, and review the leading inventors and applicants. We also provide an overview of the potential patent portfolio for the prokaryotic and eukaryotic transposons that are exploited by spin-off companies. Finally, we discuss the difficulties involved in tracing relevant state-of-the-art of articles and patent documents, based on the example of one of the most promising transposon systems, including all the impacts on the technological development of transposon tools.

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The fewer and the better: prioritization of populations for conservation under limited resources, a genetic study with Borderea pyrenaica (Dioscoreaceae) in the Pyrenean National Park.

Publication Date: 2010 Mar PMID: 19937090
Authors: Segarra-Moragues, J. G. - Catalan, P.
Journal: Genetica

Taxa considered under low International Union for the Conservation of Nature categories of extinction risk often represent cases of concern to conservation biology. Their high relative abundance precludes management of the entire range due to limited economical resources. Therefore, they require a cost-effective management plan. Borderea pyrenaica (Dioscoreaceae), an endemic plant of the Central Pyrenees and pre-Pyrenees, reaches the French side of the Central Pyrenees on its narrow northernmost boundary at Gavarnie (Parc National des Pyrenees, PNP, France), where it is protected as Vulnerable and considered a priority species. We have used nuclear microsatellite population genetic data to design a management strategy for the 11 populations of B. pyrenaica present in this area and to identify Relevant Genetic Units for its Conservation. The 18 SSR loci analysed identified 56 alleles, 24 of which fulfilled the rarity criterion for this set of populations. Genetic structuring of populations and representativity values derived from regression analyses of probabilities of loss of rare alleles together support differentiation of the B. pyrenaica populations into different management units. Estimates derived from G(ST) values indicate that five populations would adequately represent the 99.9% of the variation relative to most common alleles whereas calculations based on representativity values indicated that these five populations should equate the proportion 2:2:1 from the three different phylogeographical subdivisions of Gavarnie (Western, Eastern-1 and Eastern-2 ranges). This scheme would allow the preservation of 98.21% of the total B. pyrenaica alleles present in Gavarnie, according to the post glacial history of its populations. This conservation genetic approach could be applied to other low-extinction risk categories of extremely rare and subalpine plants in need of regulatory plans in European National Parks and Natural Reserves.

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Evolutionary dynamics of rDNA clusters on chromosomes of moths and butterflies (Lepidoptera).

Publication Date: 2010 Mar PMID: 19921441
Authors: Nguyen, P. - Sahara, K. - Yoshido, A. - Marec, F.
Journal: Genetica

We examined chromosomal distribution of major ribosomal DNAs (rDNAs), clustered in the nucleolar organizer regions (NORs), in 18 species of moths and butterflies using fluorescence in situ hybridization with a codling moth (Cydia pomonella) 18S rDNA probe. Most species showed one or two rDNA clusters in their haploid karyotype but exceptions with 4-11 clusters also occurred. Our results in a compilation with previous data revealed dynamic evolution of rDNA distribution in Lepidoptera except Noctuoidea, which showed a highly uniform rDNA pattern. In karyotypes with one NOR, interstitial location of rDNA prevailed, whereas two-NOR karyotypes showed mostly terminally located rDNA clusters. A possible origin of the single interstitial NOR by fusion between two NOR-chromosomes with terminal rDNA clusters lacks support in available data. In some species, spreading of rDNA to new, mostly terminal chromosome regions was found. The multiplication of rDNA clusters without alteration of chromosome numbers rules out chromosome fissions as a major mechanism of rDNA expansion. Based on rDNA dynamics in Lepidoptera and considering the role of ordered nuclear architecture in karyotype evolution, we propose ectopic recombination, i.e., homologous recombination between repetitive sequences of non-homologous chromosomes, as a primary motive force in rDNA repatterning.

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The impact of genome defense on mobile elements in Microbotryum.

Publication Date: 2010 Mar PMID: 19898943
Authors: Johnson, L. J. - Giraud, T. - Anderson, R. - Hood, M. E.
Journal: Genetica

Repeat induced point mutation (RIP), a mechanism causing hypermutation of repetitive DNA sequences in fungi, has been described as a 'genome defense' which functions to inactivate mobile elements and inhibit their deleterious effects on genome stability. Here we address the interactions between RIP and transposable elements in the Microbotryum violaceum species complex. Ten strains of M. violaceum, most of which belong to different species of the fungus, were all found to contain intragenomic populations of copia-like retrotransposons. Intragenomic DNA sequence variation among the copia-like elements was analyzed for evidence of RIP. Among species with RIP, there was no significant correlation between the frequency of RIP-induced mutations and inferred transposition rate based on diversity. Two strains of M. violaceum, from two different plant species but belonging to the same fungal lineage, contained copia-like elements with very low diversity, as would result from a high transposition rate, and these were also unique in showing no evidence of the hypermutation patterns indicative of the RIP genome defense. In this species, evidence of RIP was also absent from a Class II helitron-like transposable element. However, unexpectedly the absolute repetitive element load was lower than in other strains.

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Identification of sexually dimorphic gene expression in brain tissue of the fish Leporinus macrocephalus through mRNA differential display and real time PCR analyses.

Publication Date: 2010 Mar PMID: 19890727
Authors: Alves-Costa, F. A. - Wasko, A. P.
Journal: Genetica

Differentially expressed genes in males and females of vertebrate species generally have been investigated in gonads and, to a lesser extent, in other tissues. Therefore, we attempted to identify sexually dimorphic gene expression in the brains of adult males and females of Leporinus macrocephalus, a gonochoristic fish species that presents a ZZ/ZW sex determination system, throughout a comparative analysis using differential display reverse transcriptase-PCR and real-time PCR. Four cDNA fragments were characterized, representing candidate genes with differential expression between the samples. Two of these fragments presented no significant identity with previously reported gene sequences. The other two fragments, isolated from male specimens, were associated to the gene that codes for the protein APBA2 (amyloid beta (A4) precursor protein-binding, family A, member 2) and to the Rab 37 gene, a member of the Ras oncogene family. The overexpression of these genes has been associated to a greater production of the beta-amyloid protein which, in turns, is the major factor that leads to Alzheimer's disease, and to the development of brain-tumors, respectively. Quantitative RT-PCR analyses revealed a higher Apba2 gene expression in males, thus validating the previous data on differential display. L. macrocephalus may represent an interesting animal model to the understanding of the function of several vertebrate genes, including those involved in neurodegenerative and cancer diseases.

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The effect of the mus309 mutation, defective in DNA double-strand break repair, on crossing over in Drosophila melanogaster suggests a mechanism for the centromere effect of crossing over.

Publication Date: 2010 Mar PMID: 19882364
Authors: Portin, P.
Journal: Genetica

The mus309 gene in Drosophila melanogaster encodes a RecQ helicase which is involved in DNA double-strand break (DSB) repair. In a brood pattern analysis, it was observed that in mus309 mutant females, the frequency of single crossovers in the central cv-v interval of the X chromosome was reduced in young females but returned to the level of the wild type control as the females aged. In the proximal v-f interval, the frequency of single crossovers was increased during the entire experimental period. In particular, it was observed that the frequency of double crossovers, as well as the coefficient of coincidence first increased but then gradually decreased, finally reaching the level of the control flies, as the females aged. Map distances increased due to the mus309 mutation in both gene interval studies, but they did not change as the females aged, a result suggesting that the mus309 gene controls the distribution of DSBs to be repaired as crossovers instead of non-crossovers. The results suggest a mechanism for the centromere effect of crossing over in Drosophila, viz the fact the frequency of meiotic crossing over reduces with the age of the female, and that the reduction is more pronounced the closer the interval is to the proximal heterochromatin of the chromosome arm. According to the model suggested, the centromere effect is simply a matter of the balance between different pathways of the repair of the DSBs of DNA.

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B-chromosome frequency stability in Prochilodus lineatus (Characiformes, Prochilodontidae).

Publication Date: 2010 Mar PMID: 19882308
Authors: Voltolin, T. A. - Senhorini, J. A. - Oliveira, C. - Foresti, F. - Bortolozzi, J. - Porto-Foresti, F.
Journal: Genetica

The genus Prochilodus includes individuals ranging in size from medium to large, being highly relevant for commercial and subsistence fishing. Prochilodus species have a diploid number of 2n = 54 chromosomes and up to seven supernumerary (B) microchromosomes. Previous research has shown that B frequency increased drastically in the Mogi-Guacu river population of Prochilodus lineatus in the early 1980s, whereas it remained about constant in the 1990s. Here we analyses B frequency in this population during the 2003-2007 period and have found that frequency has not changed significantly since 1987, and that these B chromosomes do not show the intra-individual variation in number that characterized them in the 1980s. This indicates that these B chromosomes have been neutralized, after their invasion, through their mitotic stabilization.

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A transposon toolkit for gene transfer and mutagenesis in protozoan parasites.

Publication Date: 2010 Mar PMID: 19763844
Authors: Damasceno, J. D. - Beverley, S. M. - Tosi, L. R.
Journal: Genetica

Protozoan parasites affect millions of people around the world. Treatment and control of these diseases are complicated partly due to the intricate biology of these organisms. The interactions of species of Plasmodium, Leishmania and trypanosomes with their hosts are mediated by an unusual control of gene expression that is not fully understood. The availability of the genome sequence of these protozoa sets the stage for using more comprehensive, genome-wide strategies to study gene function. Transposons are effective tools for the systematic introduction of genetic alterations and different transposition systems have been adapted to study gene function in these human pathogens. A mariner transposon toolkit for use in vivo or in vitro in Leishmania parasites has been developed and can be used in a variety of applications. These modified mariner elements not only permit the inactivation of genes, but also mediate the rescue of translational gene fusions, bringing a major contribution to the investigation of Leishmania gene function. The piggyBac and Tn5 transposons have also been shown to mobilize across Plasmodium spp. genomes circumventing the current limitations in the genetic manipulation of these organisms.

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