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      Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood

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          Abstract

          Abstract

          Phragmotic or “door head” ants have evolved independently in several ant genera across the world, but in Africa only one case has been documented until now. Carebara elmenteitae (Patrizi) is known from only a single phragmotic major worker collected from sifted leaf-litter near Lake Elmenteita in Kenya, but here the worker castes of two species collected from Kakamega Forest, a small rainforest in Western Kenya, are studied. Phragmotic major workers were previously identified as Carebara elmenteitae and non-phragmotic major and minor workers were assigned to Carebara thoracica (Weber). Using evidence of both morphological and next-generation sequencing analysis, it is shown that phragmotic and non-phragmotic workers of the two different species are actually the same and that neither name – Carebara elmenteitae or Carebara thoracica – correctly applies to them. Instead, this and another closey related species from Ivory Coast are both morphologically different from Carebara elmenteitae , and thus they are described as the new species Carebara phragmotica sp. n. and Carebara lilith sp. n.

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          The evolution of myrmicine ants: phylogeny and biogeography of a hyperdiverse ant clade (Hymenoptera: Formicidae)

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            Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics

            Ancient and archival DNA samples are valuable resources for the study of diverse historical processes. In particular, museum specimens provide access to biotas distant in time and space, and can provide insights into ecological and evolutionary changes over time. However, archival specimens are difficult to handle; they are often fragile and irreplaceable, and typically contain only short segments of denatured DNA. Here we present a set of tools for processing such samples for state-of-the-art genetic analysis. First, we report a protocol for minimally destructive DNA extraction of insect museum specimens, which produced sequenceable DNA from all of the samples assayed. The 11 specimens analyzed had fragmented DNA, rarely exceeding 100 bp in length, and could not be amplified by conventional PCR targeting the mitochondrial cytochrome oxidase I gene. Our approach made these samples amenable to analysis with commonly used next-generation sequencing-based molecular analytic tools, including RAD-tagging and shotgun genome re-sequencing. First, we used museum ant specimens from three species, each with its own reference genome, for RAD-tag mapping. Were able to use the degraded DNA sequences, which were sequenced in full, to identify duplicate reads and filter them prior to base calling. Second, we re-sequenced six Hawaiian Drosophila species, with millions of years of divergence, but with only a single available reference genome. Despite a shallow coverage of 0.37±0.42 per base, we could recover a sufficient number of overlapping SNPs to fully resolve the species tree, which was consistent with earlier karyotypic studies, and previous molecular studies, at least in the regions of the tree that these studies could resolve. Although developed for use with degraded DNA, all of these techniques are readily applicable to more recent tissue, and are suitable for liquid handling automation.
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              Generalized DNA Barcode Design Based on Hamming Codes

              The diversity and scope of multiplex parallel sequencing applications is steadily increasing. Critically, multiplex parallel sequencing applications methods rely on the use of barcoded primers for sample identification, and the quality of the barcodes directly impacts the quality of the resulting sequence data. Inspection of the recent publications reveals a surprisingly variable quality of the barcodes employed. Some barcodes are made in a semi empirical fashion, without quantitative consideration of error correction or minimal distance properties. After systematic comparison of published barcode sets, including commercially distributed barcoded primers from Illumina and Epicentre, methods for improved, Hamming code-based sequences are suggested and illustrated. Hamming barcodes can be employed for DNA tag designs in many different ways while preserving minimal distance and error-correcting properties. In addition, Hamming barcodes remain flexible with regard to essential biological parameters such as sequence redundancy and GC content. Wider adoption of improved Hamming barcodes is encouraged in multiplex parallel sequencing applications.
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                Author and article information

                Journal
                Zookeys
                Zookeys
                ZooKeys
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2015
                5 October 2015
                : 525
                : 77-105
                Affiliations
                [1 ]Okinawa Institute of Science and Technology Graduate University, 1919–1 Tancha, Onna-son 904–0495, Japan
                [2 ]División de Entomologia, Centro de Ecologia y Biodiversidad, CEBIO. Lima, PERU
                [3 ]Department of Natural History – Zoology, Hessisches Landesmuseum Darmstadt, Friedensplatz 1, 64283 Darmstadt, Germany
                [4 ]Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 830 N University Street, Ann Arbor, MI 48701, USA
                Author notes
                Corresponding author: Georg Fischer ( georgf81@ 123456gmail.com )

                Academic editor: M. Borowiec

                Article
                10.3897/zookeys.525.6057
                4607851
                bc0378ac-6b71-4e66-b341-c78d64b8ee27
                Georg Fischer, Frank Azorsa, Francisco Hita Garcia, Alexander S. Mikheyev, Evan P. Economo

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 23 May 2015
                : 17 September 2015
                Categories
                Research Article

                Animal science & Zoology
                phragmosis,new species descriptions,hymenoptera,formicidae,carebara lilith,carebara phragmotica,worker polymorphism,rad-seq,afrotropics,kenya,ivory coast,animalia

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