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      Species Delimitation and Phylogenetic Relationships in Ectobiid Cockroaches (Dictyoptera, Blattodea) from China

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          Abstract

          We collected Ectobiidae cockroach specimens from 44 locations in the south of the Yangtze valley. We obtained 297 COI sequences specimens and carried out phylogenetic and divergence dating analyses, as well as species delimitation analysis using a General Mixed Yule Coalescent (GMYC) framework. The intraspecific and interspecific sequence divergence in Ectobiidae cockroaches ranged from 0.0 to 7.0% and 4.6 to 30.8%, respectively. GMYC analysis resulted in 53 (confidence interval: 37–65) entities (likelihood ratio = 103.63) including 14 downloaded species. The COI GMYC groups partly corresponded to the ectobiid species and 52 ectobiid species were delimited successfully based on the combination of GMYC result with morphological information. We used the molecular data and 6 cockroach fossil calibrations to obtain a preliminary estimate of the timescale of ectobiid evolution. The major subfamilies in the group were found to have diverged between ~125–110 Ma, and morphospecies pairs were found to have diverged ~10 or more Ma.

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          DNA barcodes distinguish species of tropical Lepidoptera.

          Although central to much biological research, the identification of species is often difficult. The use of DNA barcodes, short DNA sequences from a standardized region of the genome, has recently been proposed as a tool to facilitate species identification and discovery. However, the effectiveness of DNA barcoding for identifying specimens in species-rich tropical biotas is unknown. Here we show that cytochrome c oxidase I DNA barcodes effectively discriminate among species in three Lepidoptera families from Area de Conservación Guanacaste in northwestern Costa Rica. We found that 97.9% of the 521 species recognized by prior taxonomic work possess distinctive cytochrome c oxidase I barcodes and that the few instances of interspecific sequence overlap involve very similar species. We also found two or more barcode clusters within each of 13 supposedly single species. Covariation between these clusters and morphological and/or ecological traits indicates overlooked species complexes. If these results are general, DNA barcoding will significantly aid species identification and discovery in tropical settings.
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            Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections.

            We DNA barcoded 2,597 parasitoid wasps belonging to 6 microgastrine braconid genera reared from parapatric tropical dry forest, cloud forest, and rain forest in Area de Conservación Guanacaste (ACG) in northwestern Costa Rica and combined these data with records of caterpillar hosts and morphological analyses. We asked whether barcoding and morphology discover the same provisional species and whether the biological entities revealed by our analysis are congruent with wasp host specificity. Morphological analysis revealed 171 provisional species, but barcoding exposed an additional 142 provisional species; 95% of the total is likely to be undescribed. These 313 provisional species are extraordinarily host specific; more than 90% attack only 1 or 2 species of caterpillars out of more than 3,500 species sampled. The most extreme case of overlooked diversity is the morphospecies Apanteles leucostigmus. This minute black wasp with a distinctive white wing stigma was thought to parasitize 32 species of ACG hesperiid caterpillars, but barcoding revealed 36 provisional species, each attacking one or a very few closely related species of caterpillars. When host records and/or within-ACG distributions suggested that DNA barcoding had missed a species-pair, or when provisional species were separated only by slight differences in their barcodes, we examined nuclear sequences to test hypotheses of presumptive species boundaries and to further probe host specificity. Our iterative process of combining morphological analysis, ecology, and DNA barcoding and reiteratively using specimens maintained in permanent collections has resulted in a much more fine-scaled understanding of parasitoid diversity and host specificity than any one of these elements could have produced on its own.
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              Sequence-based species delimitation for the DNA taxonomy of undescribed insects.

              Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique ("diagnostic") characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.
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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 January 2017
                2017
                : 12
                : 1
                : e0169006
                Affiliations
                [1 ]College of Plant Protection, Southwest University, Beibei, Chongqing, P. R. China
                [2 ]School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
                Sichuan University, CHINA
                Author notes

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

                • Conceptualization: ZQW YLC.

                • Data curation: SHG.

                • Formal analysis: YLC AR.

                • Funding acquisition: ZQW YLC.

                • Investigation: SHG ZQW.

                • Methodology: ZQW YLC NL.

                • Project administration: ZQW YLC.

                • Resources: ZQW.

                • Software: YLC AR.

                • Supervision: ZQW.

                • Validation: YLC SHG NL AR ZQW.

                • Visualization: YLC.

                • Writing – original draft: YLC SHG.

                • Writing – review & editing: NL AR.

                Author information
                http://orcid.org/0000-0002-6295-7372
                Article
                PONE-D-16-15298
                10.1371/journal.pone.0169006
                5207705
                28046038
                931e25e0-548f-4839-9288-fcb005dfa260
                © 2017 Che 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
                : 15 April 2016
                : 10 December 2016
                Page count
                Figures: 7, Tables: 3, Pages: 25
                Funding
                Funded by: the National Natural Sciences Foundation of China
                Award ID: 31672329
                Award Recipient :
                Funded by: the National Natural Sciences Foundation of China
                Award ID: 31472026
                Award Recipient :
                Funded by the National Natural Sciences Foundation of China (Nos. 31093430, 31493021, 31672329 to Wang ZQ and 31472026 to Che YL) http://www.nsfc.gov.cn and Natural Science Foundation Project of Chongqing No. cstc2014jcyjA80018 to Wang ZQ http://www.cstc.gov.cn.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Animals
                Invertebrates
                Arthropoda
                Insects
                Cockroaches
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Processes
                Speciation
                Species Delimitation
                Biology and Life Sciences
                Anatomy
                Reproductive System
                Genital Anatomy
                Medicine and Health Sciences
                Anatomy
                Reproductive System
                Genital Anatomy
                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
                Developmental Biology
                Life Cycles
                Nymphs
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Biology and Life Sciences
                Paleontology
                Fossils
                Fossil Calibration
                Earth Sciences
                Paleontology
                Fossils
                Fossil Calibration
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
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                All relevant data are within the paper and its Supporting Information files.

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