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      Subspecific Differentiation Events of Montane Stag Beetles (Coleoptera, Lucanidae) Endemic to Formosa Island

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          Abstract

          Taxonomic debates have been carrying on for decades over Formosan stag beetles, which consist of a high proportion of endemic species and subspecies featuring morphological variations associated with local adaptation. With the influence of periodical Pleistocene glaciations and the presence of several mountain ranges, the genetic differentiation and taxonomic recognition, within this medium-size island, of two endemic subspecies for each of four montane stag beetles, i.e. Lucanus ogakii, L. kanoi, Prismognathus davidis, and Neolucanus doro, has been an appealing issue. Based on monophyletic lineages and population structure, possible divergent scenarios have been proposed to clarify the subspecific status for each of the above mentioned stag beetles. Phylogenetic inferences based on COI+16S rDNA+28S rDNA of 240 Formosan lucanids have confirmed most species are monophyletic groups; and the intraspecific (<2%) and interspecific (>2%) genetic distances of the two mitochondrial genes could be applied concordantly for taxonomic identification. On account of Bayesian-based species delimitation, geographic distribution, population structure, and sequence divergences, the subspecific status for L. ogakii, L. kanoi, and Pri. davidis are congruent with their geographic distribution in this island; and the calibration time based on the mitochondrial genes shows the subspecific split events occurred 0.7–1 million years ago. In addition, a more complicated scenario, i.e. genetic differentiation including introgression/hybridization events, might have occurred among L. ogakii, L. kanoi, and L. maculifemoratus. The geological effects of mountain hindrance accompanied by periodical glaciations could have been vital in leading to the geographical subspecific differentiation of these montane stag beetles.

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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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            Does the DNA barcoding gap exist? – a case study in blue butterflies (Lepidoptera: Lycaenidae)

            Background DNA barcoding, i.e. the use of a 648 bp section of the mitochondrial gene cytochrome c oxidase I, has recently been promoted as useful for the rapid identification and discovery of species. Its success is dependent either on the strength of the claim that interspecific variation exceeds intraspecific variation by one order of magnitude, thus establishing a "barcoding gap", or on the reciprocal monophyly of species. Results We present an analysis of intra- and interspecific variation in the butterfly family Lycaenidae which includes a well-sampled clade (genus Agrodiaetus) with a peculiar characteristic: most of its members are karyologically differentiated from each other which facilitates the recognition of species as reproductively isolated units even in allopatric populations. The analysis shows that there is an 18% overlap in the range of intra- and interspecific COI sequence divergence due to low interspecific divergence between many closely related species. In a Neighbour-Joining tree profile approach which does not depend on a barcoding gap, but on comprehensive sampling of taxa and the reciprocal monophyly of species, at least 16% of specimens with conspecific sequences in the profile were misidentified. This is due to paraphyly or polyphyly of conspecific DNA sequences probably caused by incomplete lineage sorting. Conclusion Our results indicate that the "barcoding gap" is an artifact of insufficient sampling across taxa. Although DNA barcodes can help to identify and distinguish species, we advocate using them in combination with other data, since otherwise there would be a high probability that sequences are misidentified. Although high differences in DNA sequences can help to identify cryptic species, a high percentage of well-differentiated species has similar or even identical COI sequences and would be overlooked in an isolated DNA barcoding approach.
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              Neotropical biodiversity: timing and potential drivers.

              The origin of extant neotropical biodiversity has been a controversial topic since the time of Darwin. In this review, I discuss the timing of, and potential driving factors associated with, diversification using recent evidence from molecular phylogenetics. Although these studies provide new insights into the subject, they are sensitive to dating approaches and targets, and can eventually lead to biased conclusions. A careful analysis suggests that the origin of extant neotropical biodiversity cannot be attributed to the action of one or few events during key time intervals. Rather, it is the result of complex ecological and evolutionary trends initiated by Neogene tectonic events and palaeogeographical reorganisations, and maintained by the action of Pleistocene climatic changes. Copyright © 2011 Elsevier Ltd. All rights reserved.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                3 June 2016
                2016
                : 11
                : 6
                : e0156600
                Affiliations
                [001]Department of Entomology, National Chung Hsing University, Taichung, Taiwan
                National Cheng-Kung University, TAIWAN
                Author notes

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

                Conceived and designed the experiments: CLT WBY. Performed the experiments: CLT. Analyzed the data: CLT. Contributed reagents/materials/analysis tools: CLT WBY. Wrote the paper: CLT WBY. Specimen collections: CLT.

                Author information
                http://orcid.org/0000-0003-4319-686X
                Article
                PONE-D-15-51982
                10.1371/journal.pone.0156600
                4892689
                27257861
                a4037b5e-4a79-4fde-99b3-b0e048d5e16c
                © 2016 Tsai, Yeh

                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
                : 30 November 2015
                : 17 May 2016
                Page count
                Figures: 8, Tables: 1, Pages: 23
                Funding
                These authors have no support or funding to report.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Animals
                Invertebrates
                Arthropoda
                Insects
                Beetles
                Biology and Life Sciences
                Taxonomy
                Computer and Information Sciences
                Data Management
                Taxonomy
                Biology and Life Sciences
                Paleontology
                Paleogenetics
                Earth Sciences
                Paleontology
                Paleogenetics
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Processes
                Speciation
                Species Delimitation
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Phylogenetic Analysis
                Research and Analysis Methods
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Phylogenetic Analysis
                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
                Earth Sciences
                Geology
                Geologic Time
                Cenozoic Era
                Quaternary Period
                Pleistocene Epoch
                People and Places
                Geographical Locations
                Asia
                Taiwan
                Custom metadata
                All sequences were deposited in GenBank under the inclusive following accession numbers (COI: LC074471–LC074690, LC091038–LC091039; 16S rDNA: LC074974–LC075188, LC091040–LC091041; 28S rDNA: LC066683–LC066936, LC126100–LC126101); wingless: LC077663–LC077693, LC126084–LC126099).

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