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      A tale of swinger insects: Signatures of past sexuality between divergent lineages of a parthenogenetic weevil revealed by ribosomal intraindividual variation

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          Abstract

          Naupactus cervinus (Boheman) (Curculionidae, Naupactini) is a parthenogenetic weevil native to the Paranaense Forest which displays high levels of genetic variation. Two divergent clades were identified, one ranging in forest areas (Forest clade), and the other in open vegetation areas (Grassland clade). Both of them have individuals with high levels of heterozygosity in ribosomal sequences. Investigation of intraindividual variation in ITS1 sequences through cloning and posterior sequencing suggested that mating between both groups most likely occurred in the Paranaense Forest after a secondary contact, which led to fixed heterozygotes as a consequence of parthenogenesis. Otherwise, sexual segregation would have disrupted multilocus genotypes. Only a small number of heterozygous genotypes of all the possible combinations are found in nature. We propose the occurrence of a hybrid zone in the Paranaense Forest. The fact that it is one of the most important biodiversity hotspots of the world, together with its key role for investigating evolutionary processes, makes it worthy of conservation. This is the first genetic evidence of bisexuality in N. cervinus.

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          Concerted and birth-and-death evolution of multigene families.

          Until around 1990, most multigene families were thought to be subject to concerted evolution, in which all member genes of a family evolve as a unit in concert. However, phylogenetic analysis of MHC and other immune system genes showed a quite different evolutionary pattern, and a new model called birth-and-death evolution was proposed. In this model, new genes are created by gene duplication and some duplicate genes stay in the genome for a long time, whereas others are inactivated or deleted from the genome. Later investigations have shown that most non-rRNA genes including highly conserved histone or ubiquitin genes are subject to this type of evolution. However, the controversy over the two models is still continuing because the distinction between the two models becomes difficult when sequence differences are small. Unlike concerted evolution, the model of birth-and-death evolution can give some insights into the origins of new genetic systems or new phenotypic characters.
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            Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration.

            Phylogenetic trees in insects are frequently dated by applying a "standard" mitochondrial DNA (mtDNA) clock estimated at 2.3% My(-1), but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the western and eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome oxidase I (cox1) for six codistributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (cox1, 16S rRNA) and nuclear (Mp20, 28S rRNA) genes. Six nodes marked geographically congruent east-west splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9-12 Mya. Based on these "known" dates, a divergence rate of 3.54% My(-1) for the cox1 gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intraspecific with interspecific data, and not accounting for variance in coalescent times or postseparation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineage-specific differences in rates when comparing data from various sources.
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              Simple methods for testing the molecular evolutionary clock hypothesis.

              F Tajima (1993)
              Simple statistical methods for testing the molecular evolutionary clock hypothesis are developed which can be applied to both nucleotide and amino acid sequences. These methods are based on the chi-square test and are applicable even when the pattern of substitution rates is unknown and/or the substitution rate varies among different sites. Furthermore, some of the methods can be applied even when the outgroup is unknown. Using computer simulations, these methods were compared with the likelihood ratio test and the relative rate test. The results indicate that the powers of the present methods are similar to those of the likelihood ratio test and the relative rate test, in spite of the fact that the latter two tests assume that the pattern of substitution rates follows a certain model and that the substitution rate is the same among different sites, while such assumptions are not necessary to apply the present methods. Therefore, the present methods might be useful.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: Resources
                Role: InvestigationRole: Methodology
                Role: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                2 May 2018
                2018
                : 13
                : 5
                : e0195551
                Affiliations
                [1 ] Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires—IEGEBA (CONICET-UBA), Buenos Aires, Argentina
                [2 ] Laboratorio de Agrobiotecnología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires e Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA—CONICET/UBA), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
                [3 ] División Entomología, Museo de La Plata, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata—CONICET, La Plata, Buenos Aires, Argentina
                University of Innsbruck, AUSTRIA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0001-5967-2045
                Article
                PONE-D-17-43352
                10.1371/journal.pone.0195551
                5931498
                29718921
                d11c3bb4-1eeb-4605-80c4-9d473afb97b1
                © 2018 Rodriguero et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 11 December 2017
                : 23 March 2018
                Page count
                Figures: 3, Tables: 2, Pages: 15
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100006668, Fondo para la Investigación Científica y Tecnológica;
                Award ID: 0962
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100006668, Fondo para la Investigación Científica y Tecnológica;
                Award ID: 1468
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100005363, Universidad de Buenos Aires;
                Award ID: 20020100100186
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100002923, Consejo Nacional de Investigaciones Científicas y Técnicas;
                Award ID: 112-201101-00586
                Award Recipient :
                This work was supported by Agencia Nacional de Promoción Científica y Tecnológica (Fondo para la Investigación Científica y Tecnológica), grant No. 0962, http://www.agencia.mincyt.gob.ar/frontend/agencia/fondo/foncyt (awarded to MSR); Agencia Nacional de Promoción Científica y Tecnológica (Fondo para la Investigación Científica y Tecnológica), grant No. 1468, http://www.agencia.mincyt.gob.ar/frontend/agencia/fondo/foncyt (awarded to VAC); Consejo Nacional de Investigaciones Científicas y Técnicas, grant No. 112-201101-00586, http://proyectosinv.conicet.gov.ar/ (awarded to VAC); Universidad de Buenos Aires, grant no. 20020100100186, http://cyt.rec.uba.ar/Paginas/Financiamiento/Subsidios.aspx (awarded to VAC), and a travel grant from the University of Buenos Aires (awarded to MSR). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Ecology
                Plant Ecology
                Plant Communities
                Grasslands
                Ecology and Environmental Sciences
                Ecology
                Plant Ecology
                Plant Communities
                Grasslands
                Biology and Life Sciences
                Plant Science
                Plant Ecology
                Plant Communities
                Grasslands
                Ecology and Environmental Sciences
                Terrestrial Environments
                Grasslands
                Biology and Life Sciences
                Genetics
                Heredity
                Genetic Mapping
                Variant Genotypes
                Biology and Life Sciences
                Biochemistry
                Bioenergetics
                Energy-Producing Organelles
                Mitochondria
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Energy-Producing Organelles
                Mitochondria
                Biology and Life Sciences
                Genetics
                Heredity
                Genetic Mapping
                Haplotypes
                Biology and Life Sciences
                Agriculture
                Pests
                Insect Pests
                Weevils
                Biology and Life Sciences
                Ecology
                Ecosystems
                Forests
                Ecology and Environmental Sciences
                Ecology
                Ecosystems
                Forests
                Ecology and Environmental Sciences
                Terrestrial Environments
                Forests
                Biology and Life Sciences
                Developmental Biology
                Fertilization
                Parthenogenesis
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Alleles
                Custom metadata
                All sequence files are available from the GenBank database ( https://www.ncbi.nlm.nih.gov/nuccore). Accession numbers are as follows: GQ406826.1, JX440501.1- JX4405035.1, JX440498.1, GQ406818.1, GQ406824.1, GQ406825.1, KX074094.1, KX074088.1, KX074089.1, KY305942.1, GQ406829.1 and GQ406831.1.

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