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      A Molecular Phylogeny of the Chalcidoidea (Hymenoptera)

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          Abstract

          Chalcidoidea (Hymenoptera) are extremely diverse with more than 23,000 species described and over 500,000 species estimated to exist. This is the first comprehensive phylogenetic analysis of the superfamily based on a molecular analysis of 18S and 28S ribosomal gene regions for 19 families, 72 subfamilies, 343 genera and 649 species. The 56 outgroups are comprised of Ceraphronoidea and most proctotrupomorph families, including Mymarommatidae. Data alignment and the impact of ambiguous regions are explored using a secondary structure analysis and automated (MAFFT) alignments of the core and pairing regions and regions of ambiguous alignment. Both likelihood and parsimony approaches are used to analyze the data. Overall there is no impact of alignment method, and few but substantial differences between likelihood and parsimony approaches. Monophyly of Chalcidoidea and a sister group relationship between Mymaridae and the remaining Chalcidoidea is strongly supported in all analyses. Either Mymarommatoidea or Diaprioidea are the sister group of Chalcidoidea depending on the analysis. Likelihood analyses place Rotoitidae as the sister group of the remaining Chalcidoidea after Mymaridae, whereas parsimony nests them within Chalcidoidea. Some traditional family groups are supported as monophyletic (Agaonidae, Eucharitidae, Encyrtidae, Eulophidae, Leucospidae, Mymaridae, Ormyridae, Signiphoridae, Tanaostigmatidae and Trichogrammatidae). Several other families are paraphyletic (Perilampidae) or polyphyletic (Aphelinidae, Chalcididae, Eupelmidae, Eurytomidae, Pteromalidae, Tetracampidae and Torymidae). Evolutionary scenarios discussed for Chalcidoidea include the evolution of phytophagy, egg parasitism, sternorrhynchan parasitism, hypermetamorphic development and heteronomy.

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          Most cited references 218

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          Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material.

          Procedures utilizing Chelex 100 chelating resin have been developed for extracting DNA from forensic-type samples for use with the PCR. The procedures are simple, rapid, involve no organic solvents and do not require multiple tube transfers for most types of samples. The extraction of DNA from semen and very small bloodstains using Chelex 100 is as efficient or more efficient than using proteinase K and phenol-chloroform extraction. DNA extracted from bloodstains seems less prone to contain PCR inhibitors when prepared by this method. The Chelex method has been used with amplification and typing at the HLA DQ alpha locus to obtain the DQ alpha genotypes of many different types of samples, including whole blood, bloodstains, seminal stains, buccal swabs, hair and post-coital samples. The results of a concordance study are presented in which the DQ alpha genotypes of 84 samples prepared using Chelex or using conventional phenol-chloroform extraction are compared. The genotypes obtained using the two different extraction methods were identical for all samples tested.
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            How many bootstrap replicates are necessary?

            Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reconstruction approaches, but we focus here on one of the most popular, maximum likelihood (ML). Because ML inference is so computationally demanding, it has proved too expensive to date to assess the impact of the number of replicates used in BS on the relative accuracy of the support values. For the same reason, a rather small number (typically 100) of BS replicates are computed in real-world studies. Stamatakis et al. recently introduced a BS algorithm that is 1 to 2 orders of magnitude faster than previous techniques, while yielding qualitatively comparable support values, making an experimental study possible. In this article, we propose stopping criteria--that is, thresholds computed at runtime to determine when enough replicates have been generated--and we report on the first large-scale experimental study to assess the effect of the number of replicates on the quality of support values, including the performance of our proposed criteria. We run our tests on 17 diverse real-world DNA--single-gene as well as multi-gene--datasets, which include 125-2,554 taxa. We find that our stopping criteria typically stop computations after 100-500 replicates (although the most conservative criterion may continue for several thousand replicates) while producing support values that correlate at better than 99.5% with the reference values on the best ML trees. Significantly, we also find that the stopping criteria can recommend very different numbers of replicates for different datasets of comparable sizes. Our results are thus twofold: (i) they give the first experimental assessment of the effect of the number of BS replicates on the quality of support values returned through BS, and (ii) they validate our proposals for stopping criteria. Practitioners will no longer have to enter a guess nor worry about the quality of support values; moreover, with most counts of replicates in the 100-500 range, robust BS under ML inference becomes computationally practical for most datasets. The complete test suite is available at http://lcbb.epfl.ch/BS.tar.bz2, and BS with our stopping criteria is included in the latest release of RAxML v7.2.5, available at http://wwwkramer.in.tum.de/exelixis/software.html.
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              The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism

              The concept of ‘Gondwana’, an ancient Southern Hemisphere supercontinent, is firmly established in geological and biogeographical models of Earth history. The term Gondwana (Gondwanaland of some authors) derives from the recognition by workers at the Indian Geological Survey in the mid- to late 19th century of a distinctive sedimentary sequence preserved in east central India. This succession, now known to range in age from Permian to Cretaceous, is lithologically and palaeontologically similar to coeval non-marine sedimentary successions developed in most of the Southern Hemisphere continents suggesting former continuity of these landmasses. Palaeomagnetic data and tectonic reconstructions suggest that the main assembly of Gondwana took place around the beginning of the Palaeozoic in near-equatorial latitudes and that the supercontinent as a whole shifted into high southern latitudes, allowing widespread glaciation by the end of the Carboniferous. From Carboniferous to Cretaceous times the southern continents had broadly similar floras but some species-level provincialism is apparent at all times. The break-up of Gondwana initiated during the Jurassic (at about 180 million years ago) and this process is continuing. The earliest rifting (crustal attenuation) within the supercontinent initiated in the west (between South America and Africa) and in general terms the rifting pattern propagated eastward with major phases of continental fragmentation in the Early Cretaceous and Late Cretaceous to Paleogene. Gondwanan floras show radical turnovers near the end of the Carboniferous, end of the Permian and the end of the Triassic that appear to be unrelated to isolation or fragmentation of the supercontinent. Throughout the late Palaeozoic and Mesozoic the high-latitude southern floras maintained a distinctly different composition to the palaeoequatorial and boreal regions even though they remained in physical connection with Laurasia for much of this time. Gondwanan floras of the Jurassic and Early Cretaceous (times immediately preceding and during break-up) were dominated by araucarian and podocarp conifers and a range of enigmatic seed-fern groups. Angiosperms became established in the region as early as the Aptian (before the final break-up events) and steadily diversified during the Cretaceous, apparently at the expense of many seed-fern groups. Hypotheses invoking vicariance or long distance dispersal to account for the biogeographic patterns evident in the floras of Southern Hemisphere continents all rely on a firm understanding of the timing and sequence of Gondwanan continental breakup. This paper aims to summarise the current understanding of the geochronological framework of Gondwanan breakup against which these biogeographic models may be tested. Most phytogeographic studies deal with the extant, angiosperm-dominated floras of these landmasses. This paper also presents an overview of pre-Cenozoic, gymnosperm-dominated, floristic provincialism in Gondwana. It documents the broad succession of pre-angiosperm floras, highlights the distinctive elements of the Early Cretaceous Gondwanan floras immediately preceding the appearance of angiosperms and suggests that latitudinal controls strongly influenced the composition of Gondwanan floras through time even in the absence of marine barriers between Gondwana and the northern continents.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2011
                3 November 2011
                07 November 2011
                : 6
                : 11
                Affiliations
                [1 ]Department of Entomology, University of California Riverside, Riverside, California, United States of America
                [2 ]INRA, Centre de Biologie et de Gestion des Populations, Montferrier-sur-Lez, France
                [3 ]Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
                American Museum of Natural History, United States of America
                Author notes

                Conceived and designed the experiments: JMH JBM. Performed the experiments: JMH JBM RAB DH JM AC J-YR PJ. Analyzed the data: JMH JBM. Wrote the paper: JMH JBM. Designed voucher database: JM.

                Article
                PONE-D-11-15706
                10.1371/journal.pone.0027023
                3207832
                22087244
                Munro 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.
                Page count
                Pages: 27
                Categories
                Research Article
                Agriculture
                Pest Control
                Integrated Control
                Biology
                Ecology
                Biodiversity
                Evolutionary Biology
                Evolutionary Systematics
                Taxonomy
                Animal Taxonomy
                Cladistics
                Molecular Systematics
                Phylogenetics
                Forms of Evolution
                Macroevolution
                Organismal Evolution
                Animal Evolution
                Animal Behavior
                Zoology
                Animal Behavior
                Animal Phylogenetics
                Animal Taxonomy
                Entomology
                Genetics and Genomics
                Ecology
                Neuroscience
                Evolutionary Biology

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