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      Paternal leakage and mtDNA heteroplasmy in Rhipicephalus spp. ticks

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          Abstract

          Paternal leakage of mitochondrial DNA (mtDNA) and heteroplasmy have been recently described in several animal species. In arthropods, by searching in the Scopus database, we found only 23 documented cases of paternal leakage. Therefore, although arthropods represent a large fraction of animal biodiversity, this phenomenon has been investigated only in a paucity of species in this phylum, thus preventing a reliable estimate of its frequency. Here, we investigated the occurrence of paternal leakage and mtDNA heteroplasmy in ticks belonging to one of the most significant tick species complexes, the so-called Rhipicephalus sanguineus sensu lato. By developing a multiplex allele-specific PCR assay targeting a fragment of the 12S rRNA ribosomal region of the mtDNA, we showed the occurrence of paternal leakage and mtDNA heteroplasmy in R. sanguineus s.l. ticks originated from experimental crosses, as well as in individuals collected from the field. Our results add a new evidence of paternal leakage in arthropods and document for the first time this phenomenon in ticks. Furthermore, they suggest the importance of using allele-specific assays when searching for paternal leakage and/or heteroplasmy, as standard sequencing methods may fail to detect the rare mtDNA molecules.

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          Hybridization and speciation.

          Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near-instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky-Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock-on effects on speciation both within and outside regions of hybridization. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.
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            Bias in template-to-product ratios in multitemplate PCR.

            Bias introduced by the simultaneous amplification of specific genes from complex mixtures of templates remains poorly understood. To explore potential causes and the extent of bias in PCR amplification of 16S ribosomal DNAs (rDNAs), genomic DNAs of two closely and one distantly related bacterial species were mixed and amplified with universal, degenerate primers. Quantification and comparison of template and product ratios showed that there was considerable and reproducible overamplification of specific templates. Variability between replicates also contributed to the observed bias but in a comparatively minor way. Based on these initial observations, template dosage and differences in binding energies of permutations of the degenerate, universal primers were tested as two likely causes of this template-specific bias by using 16S rDNA templates modified by site-directed mutagenesis. When mixtures of mutagenized templates containing AT- and GC-rich priming sites were used, templates containing the GC-rich permutation amplified with higher efficiency, indicating that different primer binding energies may to a large extent be responsible for overamplification. In contrast, gene copy number was found to be an unlikely cause of the observed bias. Similarly, amplification from DNA extracted from a natural community to which different amounts of genomic DNA of a single bacterial species were added did not affect relative product ratios. Bias was reduced considerably by using high template concentrations, by performing fewer cycles, and by mixing replicate reaction preparations.
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              Phylogeography's past, present, and future: 10 years after Avise, 2000.

              Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and population genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phylogeography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally conceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of "likelihood-free" approximate Bayesian methods should permit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the concurrent rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evolutionary biology.
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                Author and article information

                Contributors
                daniele.porretta@uniroma1.it
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                6 February 2019
                6 February 2019
                2019
                : 9
                : 1460
                Affiliations
                [1 ]GRID grid.7841.a, Department of Environmental Biology, , Sapienza University of Rome, ; Rome, Italy
                [2 ]ISNI 0000 0001 0120 3326, GRID grid.7644.1, Department of Veterinary Medicine, , University of Bari, ; 70010 Valenzano, Bari Italy
                [3 ]Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Contrada S. Pietro Piturno, 70017 Putignano, Bari, Italy
                [4 ]ISNI 0000 0001 0723 0931, GRID grid.418068.3, Department of Immunology, , Aggeu Magalhães Institute, Oswaldo Cruz Foundation, ; 50740465 Recife, Pernambuco Brazil
                Article
                38001
                10.1038/s41598-018-38001-8
                6365633
                30728407
                5be9d3ac-8d73-4969-92ea-aa243d21a199
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 5 August 2018
                : 13 December 2018
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