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      DNA barcoding unravels contrasting evolutionary history of two widespread Asian tiger moth species during the Late Pleistocene

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          Abstract

          Populations of widespread pest insects in tropical areas are characterized by a complex evolutionary history, with overlapping natural and human-mediated dispersal events, sudden expansions, and bottlenecks. Here, we provide biogeographic reconstructions for two widespread pest species in the tiger moth genus Creatonotos (Lepidoptera: Erebidae: Arctiinae) based on the mitochondrial cytochrome c oxidase subunit I ( COI) gene. The Asian Creatonotos transiens reveals shallow genetic divergence between distant populations that does not support its current intraspecific systematics with several local subspecies. In contrast, the more widespread Creatonotos gangis comprises at least three divergent subclades corresponding to certain geographic areas, i.e. Australia, Arabia + South Asia and Southeast Asia. With respect to our approximate Bayesian computation (ABC) model, the expansion of Creatonotos gangis into Australia is placed in the Late Pleistocene (~65–63 ka). This dating coincide with an approximate time of the earliest human migration into the continent (~65–54 ka) and the period of intervisibility between Timor and Australia (~65–62 ka). Our findings highlight that the drying Sunda and Sahul shelf areas likely support successful migrations of Asian taxa into Australia during the Pleistocene. The phylogeographic patterns discovered in this study can be used to improve the effectiveness of integrated pest control programs that is a task of substantial practical importance to a broad range of agricultural stakeholders.

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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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            Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0)

            Background Approximate Bayesian computation (ABC) is a recent flexible class of Monte-Carlo algorithms increasingly used to make model-based inference on complex evolutionary scenarios that have acted on natural populations. The software DIYABC offers a user-friendly interface allowing non-expert users to consider population histories involving any combination of population divergences, admixtures and population size changes. We here describe and illustrate new developments of this software that mainly include (i) inference from DNA sequence data in addition or separately to microsatellite data, (ii) the possibility to analyze five categories of loci considering balanced or non balanced sex ratios: autosomal diploid, autosomal haploid, X-linked, Y-linked and mitochondrial, and (iii) the possibility to perform model checking computation to assess the "goodness-of-fit" of a model, a feature of ABC analysis that has been so far neglected. Results We used controlled simulated data sets generated under evolutionary scenarios involving various divergence and admixture events to evaluate the effect of mixing autosomal microsatellite, mtDNA and/or nuclear autosomal DNA sequence data on inferences. This evaluation included the comparison of competing scenarios and the quantification of their relative support, and the estimation of parameter posterior distributions under a given scenario. We also considered a set of scenarios often compared when making ABC inferences on the routes of introduction of invasive species to illustrate the interest of the new model checking option of DIYABC to assess model misfit. Conclusions Our new developments of the integrated software DIYABC should be particularly useful to make inference on complex evolutionary scenarios involving both recent and ancient historical events and using various types of molecular markers in diploid or haploid organisms. They offer a handy way for non-expert users to achieve model checking computation within an ABC framework, hence filling up a gap of ABC analysis. The software DIYABC V1.0 is freely available at http://www1.montpellier.inra.fr/CBGP/diyabc.
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              Biogeography of the Indo-Australian Archipelago

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                Author and article information

                Contributors
                Role: Data curationRole: Writing – review & editing
                Role: Formal analysisRole: Methodology
                Role: Data curationRole: Writing – review & editing
                Role: ConceptualizationRole: Writing – review & editing
                Role: ConceptualizationRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                4 April 2018
                2018
                : 13
                : 4
                : e0194200
                Affiliations
                [1 ] Lab for Molecular Ecology and Phylogenetics, Northern Arctic Federal University, Arkhangelsk, Russian Federation
                [2 ] Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russian Federation
                [3 ] Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
                [4 ] Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
                Onderstepoort Veterinary Institute, SOUTH AFRICA
                Author notes

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

                Author information
                http://orcid.org/0000-0003-2955-3795
                Article
                PONE-D-17-35922
                10.1371/journal.pone.0194200
                5884489
                29617397
                67b9b7f8-133a-4ca3-9535-1b43bad04caf
                © 2018 Spitsyn 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
                : 6 October 2017
                : 27 February 2018
                Page count
                Figures: 5, Tables: 0, Pages: 15
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100006363, National Geographic Society;
                Award ID: 9821-15
                Award Recipient :
                Funded by: Federal Agency for Scientific Organizations
                Award ID: 0409-2015-0143
                Award Recipient :
                The field works and sampling were supported by the National Geographic Society (USA, grant no. 9821-15) ( http://www.nationalgeographic.com). The molecular analyses were supported by the Federal Agency for Scientific Organizations (Russia, project no. 0409-2015-0143) ( http://fano.gov.ru/en/).
                Categories
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                Biology and Life Sciences
                Biogeography
                Phylogeography
                Ecology and Environmental Sciences
                Biogeography
                Phylogeography
                Earth Sciences
                Geography
                Biogeography
                Phylogeography
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Genetics
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Genetics
                Heredity
                Genetic Mapping
                Haplotypes
                Earth Sciences
                Geology
                Geologic Time
                Cenozoic Era
                Quaternary Period
                Pleistocene Epoch
                People and Places
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                Asia
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
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                Arthropoda
                Insects
                Moths and Butterflies
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Biology and Life Sciences
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                Population Genetics
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                Population Biology
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