Large-Scale Mitochondrial DNA Analysis of the Domestic Goat Reveals Six Haplogroups with High Diversity

Background. From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species. Methodology/Principal Findings. The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HVI segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals. Conclusions/Significance. We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species

Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately

Stabilité évolutive de l'endo-symbiose bactérienne chez les Curculionoidea: une preuve supplémentaire de remplacement de symbiote dans la famille des charançons Dryophtoridae

International audienceBacterial intracellular symbiosis (endosymbiosis) is well documented in the insect world where it is believed to play a crucial role in adaptation and evolution. However, although Coleopteran insects are of huge ecological and economical interest, endosymbiont molecular analysis is limited to the Dryophthoridae family. Here, we have analyzed the intracellular symbiotic bacteria in 2 Hylobius species belonging to the Molytinae subfamily (Curculionoidea superfamily) that exhibit different features from the Dryophthoridae insects in terms of their ecology and geographical spanning. Fluorescence in situ hybridization has shown that both Hylobius species harbor rod-shaped pleiomorphic symbiotic bacteria in the oocyte and in the bacteria-bearing organ (the bacteriome), with a shape and location similar to those of the Dryophthoridae bacteriome. Phylogenetic analysis of the 16S ribosomal DNA gene sequences, using the heterogeneous model of DNA evolution, has placed the Hylobius spp. endosymbionts (H-group) at the basal position of the ancestral R-clade of Dryophthoridae endosymbionts named Candidatus Nardonella but relatively distant from the S-clade of Sitophilus spp. endosymbionts. Endosymbionts from the H-group and the R-clade evolved more quickly compared with free-living enteric bacteria and endosymbionts from the S- and D-clades of Dryophthoridae. They are AT biased (58.3% A + T), and they exhibit AT-rich insertions at the same position as previously described in the Candidatus Nardonella 16S rDNA sequence. Moreover, the host phylogenetic tree based on the mitochondrial COI gene was shown to be highly congruent with the H-group and the R-clade, the divergence of which was estimated to be around 125 MYA. These new molecular data show that endosymbiosis is old in Curculionids, going back at least to the common ancestor of Molytinae and Dryophthoridae, and is evolutionary stable, except in 2 Dryophthoridae clades, providing additional and independent supplementary evidence for endosymbiont replacement in these taxa

An <it>In silico </it>approach for the evaluation of DNA barcodes

<p>Abstract</p> <p>Background</p> <p>DNA barcoding is a key tool for assessing biodiversity in both taxonomic and environmental studies. Essential features of barcodes include their applicability to a wide spectrum of taxa and their ability to identify even closely related species. Several DNA regions have been proposed as barcodes and the region selected strongly influences the output of a study. However, formal comparisons between barcodes remained limited until now. Here we present a standard method for evaluating barcode quality, based on the use of a new bioinformatic tool that performs <it>in silico </it>PCR over large databases. We illustrate this approach by comparing the taxonomic coverage and the resolution of several DNA regions already proposed for the barcoding of vertebrates. To assess the relationship between <it>in silico </it>and <it>in vitro </it>PCR, we also developed specific primers amplifying different species of Felidae, and we tested them using both kinds of PCR</p> <p>Results</p> <p>Tests on specific primers confirmed the correspondence between <it>in silico </it>and <it>in vitro </it>PCR. Nevertheless, results of <it>in silico </it>and <it>in vitro </it>PCRs can be somehow different, also because tuning PCR conditions can increase the performance of primers with limited taxonomic coverage. The <it>in silico </it>evaluation of DNA barcodes showed a strong variation of taxonomic coverage (i.e., universality): barcodes based on highly degenerated primers and those corresponding to the conserved region of the <it>Cyt</it>-b showed the highest coverage. As expected, longer barcodes had a better resolution than shorter ones, which are however more convenient for ecological studies analysing environmental samples.</p> <p>Conclusions</p> <p><it>In silico </it>PCR could be used to improve the performance of a study, by allowing the preliminary comparison of several DNA regions in order to identify the most appropriate barcode depending on the study aims.</p

A new mode of action for fluopicolide: modification of the cellular localization of a spectrin-like protein

Fluopicolide does not show any cross resistance to other commercial oomycete fungicides. lt controls fungi resistant to phenylamides, strobilurins and dimethomorph, suggesting that fluopicolide has a novel mode of action. Zoospores swell and lyse rapidly upon treatment with fluopicolide. Irnmunolocalization studies showed that a cytoskeleton-associated protein, spectrin-like protein, was delocalized after fluopicolide treatment. This happens in both zoospores and hyphae of P. infestans. Spectrins play a role in membrane stability in mammalian cells, but are poorly characterized in fungi. Here they might have an important role in maintaining membrane integrity as well. Western blot experiments indicated the presence of spectrin-like protein in a crude extract of P. infestans and purification of the relevant proteins is ongoing. The possibility that the observed cellular delocalization of spectrin-like protein is the result of an effect on another, related target cannot be excluded yet. The role of spectrin-like proteins in oomycete development and the target of fluopicolide need further investigation.Le fluopicolide ne présente pas de résistance croisée avec les autres fongicides commerciaux actifs sur oomycètes. Il contrôle les champignons résistants aux phénylamines, aux strobilurines et au diméthomorphe, ce qui sous-entend que le fluopicolide possède un nouveau mode d'action. Les zoospores gonflent et sont lysées rapidement après traitement au fluopicolide. Les études d'immunolocalisation ont montré qu'une protéine associée au cytosquelette, protéine de type spectrine, était délocalisée après traitement au fluopicolide. Ceci se produit aussi bien au niveau des zoospores que des hyphes de P. infestans. Les spectrines jouent un rôle dans la stabilité de la membrane des cellules mammifères mais ne sont que peu caractérisées chez les champignons. Dans ce cas, elles pourraient également jouer un rôle important au niveau du maintient de l'intégrité de la membrane. Des expériences dites de «Western blot» indiquent la présence de protéines de type spectrine dans un extrait brut de P. infestans et la purification des protéines pertinentes est en cours. La possibilité que la délocalisation cellulaire observée de la protéine de type spectrine soit le résultat d'un effet sur une autre cible similaire ne peut pas être exclue à l'heure actuelle. Le rôle des protéines de type spectrine dans le développement des oomycètes ainsi que la cible du fluopicolide nécessitent de plus amples investigations