Revision of the Cales noacki species complex (Hymenoptera, Chalcidoidea, Aphelinidae)

ArticleinSystematic Entomology 39(2) · April 2014with 149 Reads
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Abstract
The genus Cales (Hymenoptera: Aphelinidae) includes 13 species worldwide, of which 10 form a highly morphologically uniform species complex with a native range in the Neotropical region. We recognize ten species previously attributed to a single Neotropical species, Cales noacki Howard, which in the strict sense is a species broadly disseminated to control woolly whitefly. A neotype is designated for C. noacki, and it is redescribed based on specimens molecularly determined to be conspecific with the neotype. Newly described species include: C. bicolor Mottern, n.sp., C. breviclava Mottern, n.sp., C. brevisensillum Mottern n.sp., C. curvigladius Mottern, n.sp., C. longiseta Mottern, n.sp., C. multisensillum Mottern n.sp., C. noyesi Mottern, n.sp., C. parvigladius Mottern, n.sp. and C. rosei Mottern, n.sp. Species are delimited based on a combination of morphological and molecular data (28S-D2 rDNA and COI). Additional specimens are included in the phylogenetic analyses and although these likely represent several new species, we lack sufficient specimen sampling to describe them at this time. Cales are highly morphologically conserved and character-poor, resulting in several cryptic species. A molecular phylogeny of the known Neotropical species based on 28S-D2–5 rDNA and a 390-bp segment of COI is included, and identification keys to males and females are provided. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:7FEB0479-9B2E-48E8-8603-4B7C2759D4EC.

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    Abstract A key is given to the world genera of the chalcidoid family Aphelinidae. Forty-four genera are accepted as valid, including three described as new, Encarsiella (type-species E.noyesi sp.n.), Hirtaphelinus (type-species H.smetanai sp.n.) and Samariola (type-species S.camerounensis sp.n.). The key is followed by a synopsis of the world genera, which includes: (1) citations of valid genera and their synonyms in chronological order; (2) total or approximate number of described species; (3) distribution in the six zoogeographical regions; (4) references mainly to major works and revisions; and (5) comments, especially on the new synonymies introduced in the present paper. The following new synonymies are proposed (the senior synonyms (valid names) are noted in parentheses): Aleurodiphilus DeBach & Rose (Encarsia Foerster); Aneristus Howard, Ataneostigma Girault, Heptacritus De Santis (Coccophagus Westwood); Artas Howard (Pteroptrix Westwood); Plastocharella Girault, Turmidiscapus Girault (Centrodora Foerster); Encyrtophyscus Blanchard, Physculus Jasnosh, Physcus Howard (Coccobius Ratzeburg); Mesidia Foerster (Aphelinus Dalman); Paranthemus Girault (Cales Howard); Primaprospaltella DeBach & LaSalle (Coccophagoides Girault). The following genera are regarded as of doubtful position: Mesopirene Girault, Neocales Risbec, Paulianaphelinus Risbec and Verekia Risbec.
  • Article
      Gollumiellinae is proposed as a new subfamily for the Indo-Pacific genera Gollumiella Hedqvist and Anorasema Bouc̆ek based on analyses of three ribosomal transcript gene regions (28S-D2 and -D3, and 18S-E23; 1262 aligned base pairs) sequenced for twenty-eight genera and fifty-four species of Eucharitidae, and twelve genera and nineteen species of Pteromalidae (Pteromalinae) and Perilampidae (Chrysolampinae and Perilampinae). Gollumiella and Anorasema have been treated as either a monophyletic or paraphyletic group within the Eucharitini (Hymenoptera: Eucharitidae). The monophyly of the Eucharitidae and a sister-group relationship between Gollumiellinae and Oraseminae + Eucharitinae are supported strongly in parsimony and Bayesian analyses. The molecular phylogeny contradicts previous morphological hypotheses, in which Gollumiella and Anorasema are within Eucharitini. The strength of the molecular hypothesis is explored through evaluations of data alignments that are eye optimized, clustal-x aligned, eye optimized but with gaps coded as a fifth base, and eye optimized and combined with morphological data. The oviposition behaviour and host associations of G. longipetiolata on tree ferns (Cyathea latebrosa, Cyatheaceae), and the morphology of the planidium and pupa are newly described. Eggs are deposited vertically, with the base anchored into the leaf or petiolar surface. Unlike other Eucharitidae, the eggs are not stalked, but rather tipped with a secretion that may act as an attractant for their ant host, Paratrechina sp. (Formicidae: Formicinae). Various morphological character state optimizations and their implications for convergent morphology, behaviour and host associations are discussed. All results using gene regions treated separately or combined with the morphological data reach the same conclusion: Anorasema + Gollumiella form the sister group of Oraseminae + Eucharitinae, and thus deserve subfamily status. This suggests that very distinct traits such as the fusion of the pronotum and prepectus in adults and the fusion of the first two tergites of the planidia are convergent apomorphies. Molecular data, when strongly supported, can provide new information to unravel convergent from synapomorphic changes, resulting in more robust hypotheses of relationship.
  • Article
    In order to investigate parasitoids of the genus Cotesia (Hymenoptera: Braconidae), larvae of a speciose group of butterflies, the tribe Melitaeini (Lepidoptera: Nymphalidae), were collected from several sites in Catalonia, northern Spain, a region that harbours ten out of the 20 European species of Melitaeini. New information on the natural history of the butterflies is presented, and the structure of their communities and patterns of larval parasitism are described. On the basis of mtDNA sequence data (COI gene), microsatellite data (ten loci) and behavioural experiments, we recognize seven biologically distinct species of Cotesia parasitizing the Melitaeini communities within this relatively small geographical area. In particular, the notional species C. melitaearum and C. acuminata each represents a series of cryptic species with narrow host associations. The possibility of direct competition among the parasitoids and/or indirect interactions between butterflies mediated by Cotesia parasitoids is explored. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 86, 45–65.
  • Article
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    So-called DNA barcodes have recently been proposed to answer the problem of specimen identification and to quantify global biodiversity. We show that this proposition is wanting in terms of rationale, methodology and interpretation of results. fit addition to falling short of all its stated goals, the method abandons the benefits of morphological Studies in favor of a limited molecular identification system that would ultimately impede our understanding of biodiversity. (C) The Willi Hennig Society 2004.
  • Article
    The usefulness of the internally transcribed spacer 2 (ITS2) of the nuclear ribosomal gene complex is tested for providing taxonomic characters to identify Trichogramma species. The ITS2 sequences of a group of sibling species of the T. deion/T. pretiosum complexes were determined. A simple and precise identification key to the species of these assemblages was constructed using as taxonomic characters the size of the ITS2 and the difference in restriction length polymorphism of species with similarly sized ITS2. Individual wasps can be identified by amplification of their ITS2 with general primers, determining the size of the PCR product using standard agarose electrophoresis, followed in some species by a DNA-digestion with a restriction enzyme. Because this system works well for a number of closely related species we are hopeful that similar PCR-based identification can be extended to all species of the genus once their ITS2 sequences have been determined. The advantage of this identification system over the morphology-based system is that non-specialists are able to quickly and cheaply identify individual specimens. In addition, species specific primers were tested for the two most common species of these groups (i.e. T. pretiosum and T. deion). These primers can be used either as a direct identification tool or as a method to confirm the identification using the general key. The phylogeny of this group of wasps was also analyzed based on the ITS2 sequence.
  • Article
    Pnigalio soemius is a polyphagous ectoparasitoid of late instars of leafminers or gallmaking larvae belonging to different orders of holometabolous insects. The aim of this work was to determine whether two populations of P. soemius obtained respectively from two lepidopteran hosts (Cosmopterix pulchrimella and Holocacista rivillei) represent a single species or two sibling species. Different complementary approaches were used: (1) uni- and multivariate analysis of morphological characters; (2) reproductive compatibility tests; (3) evaluation and comparison of different behavioral and biological traits; (4) karyological analysis (chromosome number, morphology and NORs); (5) molecular characterization of mtDNA (COI) and RFLP-PCR. Our results demonstrate the existence of two reproductively isolated cryptic species, even though their two karyotypes could not be distinguished and the morphometric analysis was only partially able to discriminate the two populations (86% with analysis of ratios and 92% with analysis of Burnaby size-adjusted data). These results point out that the broad concept of P. soemius may include cryptic species whose correct characterization plays a decisive role when evaluating the effects of field-margin habitats.
  • Article
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    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.
  • Article
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    An intense, 30-year, ongoing biodiversity inventory of Lepidoptera, together with their food plants and parasitoids, is centered on the rearing of wild-caught caterpillars in the 120,000 terrestrial hectares of dry, rain, and cloud forest of Area de Conservacion Guanacaste (ACG) in northwestern Costa Rica. Since 2003, DNA barcoding of all species has aided their identification and discovery. We summarize the process and results for a large set of the species of two speciose subfamilies of ACG skipper butterflies (Hesperiidae) and emphasize the effectiveness of barcoding these species (which are often difficult and time-consuming to identify). Adults are DNA barcoded by the Biodiversity Institute of Ontario, Guelph, Canada; and they are identified by correlating the resulting COI barcode information with more traditional information such as food plant, facies, genitalia, microlocation within ACG, caterpillar traits, etc. This process has found about 303 morphologically defined species of eudamine and pyrgine Hesperiidae breeding in ACG (about 25% of the ACG butterfly fauna) and another 44 units indicated by distinct barcodes (n = 9,094), which may be additional species and therefore may represent as much as a 13% increase. All but the members of one complex can be identified by their DNA barcodes. Addition of DNA barcoding to the methodology greatly improved the inventory, both through faster (hence cheaper) accurate identification of the species that are distinguishable without barcoding, as well as those that require it, and through the revelation of species "hidden" within what have long been viewed as single species. Barcoding increased the recognition of species-level specialization. It would be no more appropriate to ignore barcode data in a species inventory than it would be to ignore adult genitalia variation or caterpillar ecology.
  • Article
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    There is a long-standing controversial about how parthenogenetic species can be defined in absence of a generally accepted species concept for this reproductive mode. An integrative approach was suggested, combining molecular and morphological data to identify distinct monophyletic entities. Using this approach, speciation of parthenogenetic lineages was recently demonstrated for groups of bdelloid rotifers and oribatid mites. Trhypochthonius tectorum, an oribatid mite from the entirely parthenogenetic desmonomatan family Trhypochthoniidae, is traditionally treated as a single species in Central Europe. However, two new morphological lineages were recently proposed for some Austrian populations of T. tectorum, and were described as novel subspecies (T. silvestris europaeus) or form (T. japonicus forma occidentalis). We used the morphological and morphometrical data which led to this separation, and added mitochondrial and nuclear DNA sequences and the chemical composition of complex exocrine oil gland secretions to test this taxonomical hypothesis. This is the first attempt to combine these three types of data for integrative taxonomical investigations of oribatid mites. We show that the previous European species T. tectorum represents a species complex consisting of three distinct lineages in Austria (T.tectorum, T. silvestris europaeus and T. japonicus forma occidentalis), each clearly separated by morphology, oil gland secretion profiles and mitochondrial cox1 sequences. This diversification happened in the last ten million years. In contrast to these results, no variation among the lineages was found in the nuclear 18S rDNA. Our approach combined morphological, molecular and chemical data to investigate diversity and species delineation in a parthenogenetic oribatid mite species complex. To date, hypotheses of a general oribatid mite phylogeny are manifold, and mostly based on single-method approaches. Probably, the integrative approach proposed here can be used to uncover further hidden biodiversity of glandulate Oribatida and help to build up more stable phylogenetic hypotheses in the future.
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    Collections of parasitoids attacking the soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), in South Korea yielded specimens that were originally identified as Binodoxys communis (Gahan) (Hymenoptera: Braconidae). We report here on laboratory studies indicating that this population is actually a previously unknown species of Binodoxys. Four classes of comparisons were made between the Korean population and a Chinese population that also had been identified as B. communis. The comparisons included 1) mating trials coupled with behavioral observations and spermathecal examinations, 2) assessment of nucleotide divergence at two mitochondrial and two nuclear gene loci, 3) patterns of host use, and 4) reassessment of morphological characters. These studies revealed premating reproductive isolation of the two populations and minor nucleotide differences in mitochondrial cytochrome oxidase I sequences and nuclear internal transcriber spacer 1 sequences, providing strong indications that they are different species. Subtle morphological differences also were discovered that confirmed that the Chinese population corresponds to B. communis, whereas the Korean population does not. We propose the name Binodoxys koreanus StarÝ, sp. n. for the Korean population. The two species exhibited similar host ranges in the laboratory, the most notable exception being that B. koreanus, sp. n. is better able to develop in a population of Aphis craccivora Koch that harbors the bacterial endosymbiont Hamiltonella defensa Moran, which seems to strongly interfere with the development of B. communis. We discuss the implications of our results for biological control introductions against the soybean aphid in North America.
  • Article
    The two egg parasitoid species Trichogramma minutum Riley and T. platneri Nagarkatti are closely related. No morphological or molecular characters are known to distinguish them. Their treatment as distinct species rests on the absence of female offspring in between-species crosses. The current species definitions, which must be considered tentative, assume their natural ranges to differ, with T. minutum occurring east of the Rocky Mountains and T. platneri occurring to the west. Both species are used throughout North America for the biological control of moths in orchards and forests. They are available to growers and researchers through a large number of biological control suppliers. Because the species can only be identified after crosses with known cultures, it is likely that producers often cannot be sure of the identity of their wasps. Here we studied the causes of the lack of female offspring in the between-species crosses and what happened when one species is released for biological control in the native area of the other. Our results show that females in between-species crosses are inseminated and use the sperm to fertilize their eggs, but that these fertilized eggs die. In addition, females do not preferentially mate with males of their own species when exposed to conspecific and nonconspecific males. These results are used in a model to predict the effect of releasing the non-native species in the native area of the other species. This model shows that such introductions
  • Article
    Multiple alignment of DNA sequences is an important step in various molecular biological analyses. As a large amount of sequence data is becoming available through genome and other large-scale sequencing projects, scalability, as well as accuracy, is currently required for a multiple sequence alignment (MSA) program. In this chapter, we outline the algorithms of an MSA program MAFFT and provide practical advice, focusing on several typical situations a biologist sometimes faces. For genome alignment, which is beyond the scope of MAFFT, we introduce two tools: TBA and MAUVE.
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    Despite recent advances achieved by application of high-performance computing methods and novel algorithmic techniques to maximum likelihood (ML)-based inference programs, the major computational bottleneck still consists in the computation of bootstrap support values. Conducting a probably insufficient number of 100 bootstrap (BS) analyses with current ML programs on large datasets-either with respect to the number of taxa or base pairs-can easily require a month of run time. Therefore, we have developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms. These new heuristics can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses. Computational experiments to assess the performance and relative accuracy of these heuristics were conducted on 22 diverse DNA and AA (amino acid), single gene as well as multigene, real-world alignments containing 125 up to 7764 sequences. The standard BS (SBS) and rapid BS (RBS) values drawn on the best-scoring ML tree are highly correlated and show almost identical average support values. The weighted RF (Robinson-Foulds) distance between SBS- and RBS-based consensus trees was smaller than 6% in all cases (average 4%). More importantly, RBS inferences are between 8 and 20 times faster (average 14.73) than SBS analyses with RAxML and between 18 and 495 times faster than BS analyses with competing programs, such as PHYML or GARLI. Moreover, this performance improvement increases with alignment size. Finally, we have set up two freely accessible Web servers for this significantly improved version of RAxML that provide access to the 200-CPU cluster of the Vital-IT unit at the Swiss Institute of Bioinformatics and the 128-CPU cluster of the CIPRES project at the San Diego Supercomputer Center. These Web servers offer the possibility to conduct large-scale phylogenetic inferences to a large part of the community that does not have access to, or the expertise to use, high-performance computing resources.
  • Article
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    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. • Area de Conservación Guanacaste • Costa Rica • caterpillar • Braconidae • host specificity
  • Article
    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.
  • Article
    The phylogeny of the cryptic species complex of wasps in the genus Nasonia was inferred by analysis of nucleotide sequences of an rDNA internal transcribed spacer (ITS2) and the D2 region of 28S rDNA. Phylogenetic analysis showed that N. vitripennis descended from a theoretical common ancestor with that of a lineage that diverged into N. longicornis and N. giraulti. Differences in the ITS2 regions clearly distinguished two strains of N. giraulti. Another member of the Dibrachys Group, Trichomalopsis dubius, was placed outside of the Nasonia complex. The D2 region had a base substitution rate approximately 2 times slower than the ITS2 region and was used to resolve the phylogenetic affiliation of an eulophid, Melittobia digitata, to the pteromalids. Tree topology of the Nasonia complex was congruent with the phylogeny of a cluster of Wolbachia bacteria which infect these insects. The possible role of these bacteria in driving speciation is discussed.
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    Wolbachia are a group of cytoplasmically inherited bacteria that cause reproduction alterations in arthropods, including parthenogenesis, reproductive incompatibility, feminization of genetic males and male killing. Previous general surveys of insects in Panama and Britain found Wolbachia to be common, occurring in 16-22% of species. Here, using similar polymerase chain reaction methods, we report that 19.3% of a sample of temperate North American insects are infected with Wolbachia, a frequency strikingly similar to frequencies found in two other studies in widely separated locales. The results may indicate a widespread equilibrium of Wolbachia infection frequencies in insects whose maintenance remains to be explained. Alternatively, Wolbachia may be increasing in global insect communities. Within each of the three geographic regions surveyed, Hymenoptera are more frequently infected with A group Wolbachia and Lepidoptera more frequently infected with B group Wolbachia.
  • Article
    Species of Encarsia Förster (Hymenoptera: Aphelinidae, Coccophaginae) are economically important for the biological control of whitefly and armored scale pests (Hemiptera: Aleyrodidae, Diaspididae). Whereas some regional keys for identification of Encarsia species are now available, few studies have addressed relationships within this diverse and cosmopolitan genus because of unreliable morphological data. Nuclear sequences of the D2 expansion region of 28S rDNA were determined from 67 strains of 24 species representing 10 species groups of Encarsia, 2 strains of Encarsiella noyesi Hayat, and 1 strain of Coccophagoides fuscipennis Girault. Analysis of molecular data alone and combined with morphological data resolves many nodes not resolved by morphology alone and offer insights into which morphological characters are useful for supporting group relationships. All analyses that include molecular data reveal Encarsia to be paraphyletic with respect to Encarsiella. If monophyly of Encarsia is constrained, the relationships are the same but with a different root within Encarsia, and these trees are presented as an alternate hypothesis. The luteola and strenua species groups are shown by both morphological and molecular data to be monophyletic, whereas the inaron group, the E. nigricephala + luteola group, and the E. quericola + strenua group are supported only by molecular data. The aurantii and parvella species groups are not supported in any of the analyses. The utility of morphological characters for defining species group relationships is discussed.
  • Article
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    As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.
  • Article
    Several series of host-reared specimens of an Encarsia species, initially thought to be the cosmopolitan Encarsia inaron (Walker), were collected in the Azores Islands (Portugal). Subsequent morphometric analysis supported the presence of two species: E. inaron and a new species, described herein as Encarsia estrellae Manzari & Polaszek sp. n. Encarsia estrellae was reared from Aleyrodes singularis Danzig, A. ?singularis, and Bemisia sp. afer-group on several host plants. In addition, the D2 region of the 28S rDNA gene was sequenced in eight individuals belonging to these species, as well as single representatives of two closely related and one distantly related species. Phylogenetic analysis of these DNA sequences, together with 23 additional Encarsia sequences retrieved from the European Molecular Biology Laboratory (EMBL) and GenBank databases, further supported the specific status of E. estrellae, and the placement of E. dichroa (Mercet) in the E. inaron species-group. Additionally, E. inaron is redescribed and some taxonomic problems in the E. inaron species-group are discussed.
  • Article
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    MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters. Availability: http://morphbank.ebc.uu.se/mrbayes Contact: fredrik.ronquist{at}ebc.uu.se
  • Article
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    With millions of species and their life-stage transformations, the animal kingdom provides a challenging target for taxonomy. Recent work has suggested that a DNA-based identification system, founded on the mitochondrial gene, cytochrome c oxidase subunit 1 (COI), can aid the resolution of this diversity. While past work has validated the ability of COI sequences to diagnose species in certain taxonomic groups, the present study extends these analyses across the animal kingdom. The results indicate that sequence divergences at COI regularly enable the discrimination of closely allied species in all animal phyla except the Cnidaria. This success in species diagnosis reflects both the high rates of sequence change at COI in most animal groups and constraints on intraspecific mitochondrial DNA divergence arising, at least in part, through selective sweeps mediated via interactions with the nuclear genome.
  • Article
    The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximum- likelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximum-likelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distance-based and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/.
  • Article
    Mitochondrial DNA (mtDNA) has been a marker of choice for reconstructing historical patterns of population demography, admixture, biogeography and speciation. However, it has recently been suggested that the pervasive nature of direct and indirect selection on this molecule renders any conclusion derived from it ambiguous. We review here the evidence for indirect selection on mtDNA in arthropods arising from linkage disequilibrium with maternally inherited symbionts. We note first that these symbionts are very common in arthropods and then review studies that reveal the extent to which they shape mtDNA evolution. mtDNA diversity patterns are compatible with neutral expectations for an uninfected population in only 2 of 19 cases. The remaining 17 studies revealed cases of symbiont-driven reduction in mtDNA diversity, symbiont-driven increases in diversity, symbiont-driven changes in mtDNA variation over space and symbiont-associated paraphyly of mtDNA. We therefore conclude that these elements often confound the inference of an organism's evolutionary history from mtDNA data and that mtDNA on its own is an unsuitable marker for the study of recent historical events in arthropods. We also discuss the impact of these studies on the current programme of taxonomy based on DNA bar-coding.
  • Article
    The genus Encarsia Förster includes parasitoid species that are effective natural enemies of whitefly and armoured scale insect agricultural pests. Within this genus, several species groups have been recognized on the basis of morphological similarity, although their monophyly appears uncertain. It is often difficult to separate morphologically similar species, and there is evidence that some species could in fact be complexes of cryptic species. Their correct identification is fundamental for biological control purposes. Recently, due to unreliability of morphological characters, molecular techniques have been investigated to identify markers that differentiate closely related species. In this study, DNA variation in an approximately 900 bp segment of the mitochondrial cytochrome oxidase subunit I (COI) gene was examined by both sequencing and PCR-RFLP. Two pairs of species that are difficult to distinguish morphologically were analysed: Encarsia formosa Gahan and Encarsialuteola Howard, belonging to the luteola group, and two populations of Encarsiasophia (Girault & Dodd) from Pakistan and Spain, belonging to the strenua group, recently characterized as cryptic species. High sequence divergence and species-specific restriction patterns clearly differentiate both species pairs. Parsimony analysis of the nucleotide sequences was also performed, including Encarsiahispida De Santis (luteola group) and Encarsia protransvena Viggiani (strenua group). Two monophyletic clades supporting the two groups of species considered were resolved. The results of this study support the use of the COI gene as a useful marker in separating species of Encarsia, for which morphological differences are subtle. Moreover, the COI gene appears potentially useful for understanding phylogenetic relationships in this genus.
  • Article
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    DNA barcoding has attracted attention with promises to aid in species identification and discovery; however, few well-sampled datasets are available to test its performance. We provide the first examination of barcoding performance in a comprehensively sampled, diverse group (cypraeid marine gastropods, or cowries). We utilize previous methods for testing performance and employ a novel phylogenetic approach to calculate intraspecific variation and interspecific divergence. Error rates are estimated for (1) identifying samples against a well-characterized phylogeny, and (2) assisting in species discovery for partially known groups. We find that the lowest overall error for species identification is 4%. In contrast, barcoding performs poorly in incompletely sampled groups. Here, species delineation relies on the use of thresholds, set to differentiate between intraspecific variation and interspecific divergence. Whereas proponents envision a "barcoding gap" between the two, we find substantial overlap, leading to minimal error rates of approximately 17% in cowries. Moreover, error rates double if only traditionally recognized species are analyzed. Thus, DNA barcoding holds promise for identification in taxonomically well-understood and thoroughly sampled clades. However, the use of thresholds does not bode well for delineating closely related species in taxonomically understudied groups. The promise of barcoding will be realized only if based on solid taxonomic foundations.
  • Article
    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. • Area de Conservación Guanacaste • cytochrome c oxidase I • Hesperiidae • Sphingidae • Saturniidae
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    With increasing force, genetic divergence of mitochondrial DNA (mtDNA) is being argued as the primary tool for discovery of animal species. Two thresholds of single-gene divergence have been proposed: reciprocal monophyly, and 10 times greater genetic divergence between than within species (the "10x rule"). To explore quantitatively the utility of each approach, we couple neutral coalescent theory and the classical Bateson-Dobzhansky-Muller (BDM) model of speciation. The joint stochastic dynamics of these two processes demonstrate that both thresholds fail to "discover" many reproductively isolated lineages under a single incompatibility BDM model, especially when BDM loci have been subject to divergent selection. Only when populations have been isolated for > 4 million generations did these thresholds achieve error rates of < 10% under our model that incorporates variable population sizes. The high error rate evident in simulations is corroborated with six empirical data sets. These properties suggest that single-gene, high-throughput approaches to discovering new animal species will bias large-scale biodiversity surveys, particularly toward missing reproductively isolated lineages that have emerged by divergent selection or other mechanisms that accelerate reproductive isolation. Because single-gene thresholds for species discovery can result in substantial error at recent divergence times, they will misrepresent the correspondence between recently isolated populations and reproductively isolated lineages (= species).
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    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. 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. 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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    Many species of tachinid flies are viewed as generalist parasitoids because what is apparently a single species of fly has been reared from many species of caterpillars. However, an ongoing inventory of the tachinid flies parasitizing thousands of species of caterpillars in Area de Conservación Guanacaste, northwestern Costa Rica, has encountered >400 species of specialist tachinids with only a few generalists. We DNA-barcoded 2,134 flies belonging to what appeared to be the 16 most generalist of the reared tachinid morphospecies and encountered 73 mitochondrial lineages separated by an average of 4% sequence divergence. These lineages are supported by collateral ecological information and, where tested, by independent nuclear markers (28S and ITS1), and we therefore view these lineages as provisional species. Each of the 16 apparently generalist species dissolved into one of four patterns: (i) a single generalist species, (ii) a pair of morphologically cryptic generalist species, (iii) a complex of specialist species plus a generalist, or (iv) a complex of specialists with no remaining generalist. In sum, there remained 9 generalist species among the 73 mitochondrial lineages we analyzed, demonstrating that a generalist lifestyle is possible for a tropical caterpillar parasitoid fly. These results reinforce the emerging suspicion that estimates of global species richness are likely underestimates for parasitoids (which may constitute as much as 20% of all animal life) and that the strategy of being a tropical generalist parasitic fly may be yet more unusual than has been envisioned for tachinids. • 28S • Area de Conservación Guanacaste • cytochrome c oxidase 1 • internal transcribed spacer 1 • species diversity