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A revised phylogenetic analysis for the spider genus Clitaetra Simon, 1889 (Araneae, Araneoidea, Nephilidae) with the first description of the male of the Sri Lankan species Clitaetra thisbe Simon, 1903

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A revised phylogenetic analysis for the spider genus Clitaetra Simon, 1889 (Araneae, Araneoidea, Nephilidae) with the first description of the male of the Sri Lankan species Clitaetra thisbe Simon, 1903
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  A REVISED PHYLOGENETIC ANALYSIS FOR THE SPIDER GENUS CLITAETRA  SIMON, 1889 (ARANEAE, ARANEOIDEA, NEPHILIDAE)WITH THE FIRST DESCRIPTION OF THE MALE OF THE SRI LANKANSPECIES  CLITAETRA THISBE   SIMON, 1903 DIMITAR DIMITROV, 1,4 SURESH P. BENJAMIN, 2 AND GUSTAVO HORMIGA 3 A BSTRACT . In this study, we describe the previously unknown male of the spider  Clitaetra thisbe  Simon,1903, from Sri Lanka and provide some data on itsnatural history. In light of this new information, wepresent results from the first cladistic analyses of  Clitaetra  species that include male morphologicalcharacters of   C. thisbe  and DNA sequence data forrepresentatives of all nephilid genera and a broadsample of outgroups. The monophyly of   Clitaetra  andthe basal position of   C. thisbe  within the genus arecorroborated. Our results also support the hypothesisthat  Nephila  is a sister group to the clade  Herennia  + Nephilengys , which challenges the current hypothesisfor nephilid relationships that has been used exten-sively for the study of genitalic and web evolution inNephilidae. We also discuss some of the previously proposed interpretations and primary homology state-ments for several male genitalic characters in nephilids. INTRODUCTION Nephilids are orb-weaving spiders thatinhabit the tropical and subtropical regionsof the world.  Nephila  Leach, 1815, speciesare probably among the most conspicuousspiders in these geographical areas in thatfemales can reach up to about 4 cm body length and their webs often exceed 1 m indiameter (Harvey et al., 2007; Jocque´  andDippenaar-Schoeman, 2006; Robinson andRobinson, 1973). The first cladistic studiesthat included  Nephila  and its relativesplaced this araneoid lineage as sister to aclade comprising all other tetragnathidsand treated it as a subfamily withinTetragnathidae (Coddington 1990; Gris- wold et al., 1998; Hormiga et al., 1995). Arecent revisionary study elevated the groupcontaining the genera  Nephila; Herennia Thorell, 1877;  Nephilengys  L. Koch, 1872;and  Clitaetra  to family rank and refutedthe placement of nephilids as a tetra-gnathid lineage (Kuntner, 2006; see alsoKuntner et al., 2008). More recently, in astudy that featured a multilocus moleculardataset combined with morphological evi-dence, A´ lvarez-Padilla et al. (2009) alsofound that nephilids do not represent atetragnathid lineage. Kuntner (2006) alsorevised and phylogenetically tested themonophyly and the relationships of   Clitae- tra  and demonstrated that the genera Deliochus  Simon, 1894, and  Phonognatha Simon, 1894, do not belong within Nephi-lidae. The latter two genera were formally transferred to the family Araneidae by Kuntner et al. (2008).Kuntner’s (2006) revision of   Clitaetra represents the most comprehensive study of this genus to date. One of the findings of his revision is the basal phylogenetic posi-tion of the Sri Lankan species  Clitaetra thisbe  as sister to a clade that includes theremaining species in the genus. This hy-pothesis makes  C. thisbe  (Fig. 1A, B)particularly important for the polarization 4 Corresponding author. 1 Department of Biological Sciences, The George Washington University, Washington D.C. (e-mail:dimitard@gwu.edu). 2 Senior Research Fellow, Institute of FundamentalStudies, Hantana Road, Kandy, Sri Lanka (e-mail:suresh.benjamin@gmail.com). 3 Department of Biological Sciences, The George Washington University, Washington, D.C. ResearchAssociate, Department of Invertebrates, Museum of Comparative Zoology (e-mail: hormiga@gwu.edu). Bull. Mus. Comp. Zool., 159(6): 301–323, December, 2009 301  Figure 1.  Clitaetra thisbe   female from Gilimale Forest Reserve: dorsal/frontal view A/B; web C; hub detail D. Photos by SPB. 302  Bulletin of the Museum of Comparative Zoology, Vol. 159, No. 6  of nephilid characters. In this study, wedescribe the previously unknown male of   C. thisbe , correct some errors of interpretationof the female genitalic structures and revisethe phylogeny of   Clitaetra  by including thenew and revised information. Part of thematerial of   C. thisbe  (Bodinagala ForestReserve) was collected not far from its typelocality in Sri Lanka, the city of Galle. Theforests of Galle, although degraded, werenot ‘‘disastrously affected by the 2004tsunami’’ as claimed by Kuntner (2006). We also analyze multilocus sequence datafor many of the studied species. Themolecular data resulted from our ownongoing work on araneoid phylogeny (e.g.,A´ lvarez-Padilla et al., 2009; these sequencesare readily available in GenBank). Theincluded nucleotide data provide additionallines of evidence and allow a more rigoroustest of phylogenetic hypotheses.Kuntner’s (2006) classification recog-nized two subfamilies within Nephilidae:Clitaetrinae, containing the genus  Clitaetra ,and Nephilinae, containing the remainingthree nephilid genera. Clitaetrinae wasfurther split into three subgenra:  Indoetra , Clitaetra , and  Afroetra . Kuntner’s (2006)classification of   Clitaetra  has been usedrecently as a case example of a new approach to classification (Kuntner andAgnarsson, 2006). It is thus relevant toprovide some comments on the merits of this approach, and we do so in theDiscussion section of this paper. MATERIALS AND METHODS Specimens were examined with a LeicaMZ16A stereoscopic microscope with acamera lucida and Leica DMRM compoundmicroscope with a drawing tube. Drawings were done with graphite pencils on acid-free cotton paper. Hairs and macrosetae arenot depicted in the final drawings. The rightmale palp was illustrated (the only intactpalp available), and scanned images weredigitally transposed. The epigynum wastreated with SIGMA Pancreatin LP 1750enzyme complex (A´ lvarez-Padilla and Hor-miga, 2008) to digest remaining tissues andtransferred to methyl salicylate solution forexamination and drawing.All pencil drawings were scanned andfurther improved with the help of GIMP 2.4and Adobe Photoshop CS2 programs. Dig-ital images of the specimens were taken inalcohol media with a Nikon DXM1200Fdigital camera mounted on a Leica MZ16Astereoscopic microscope. The final plate’slayout and editing was done with AdobeIllustrator CS2. Webs were dusted withcornstarch for observation and photo docu-mentation. Phylogenetics Characters . The character matrix of thisstudy is taken from Kuntner’s revision of  Clitaetra  (Kuntner, 2006). After submissionof this paper for publication, Kuntner andAgnarsson (2009) published a study onIndian Ocean  Clitaetra , in which they revised some of the scorings of four web-building characters for three  Clitaetra species. Their analysis of a matrix with therevised character scores did not change the Clitaetra  cladistic topology reported inKuntner (2006) and Kuntner et al. (2008).For most of the characters, we have scoredthe male morphology of   C. thisbe  inaccordance with the original characterdefinitions of Kuntner (2006). These char-acters are discussed elsewhere (Kuntner,2006, and references therein). One discrep-ancy between our analyses and Kuntner’s work comes from differences in the inter-pretation and coding of some male pedipal-pal sclerites. Arguably the most controver-sial point in this respect is Kuntner’streatment of the sclerite in the male palpfunctioning as a conductor. He states that innephilids this sclerite, for which he uses theterm ‘‘embolic conductor,’’ is a novelstructure that is part of the embolic divisionand thus non-homologous to the araneoidconductor (Kuntner, 2005, 2006; Kuntner etal., 2008; Kuntner and Agnarsson, 2009). We disagree with this interpretation and ourrationale has been discussed elsewhere C LITAETRA  N  Dimitrov et al.  303  (Dimitrov and Hormiga, 2009; see alsoA´ lvarez-Padilla, 2007; A´ lvarez-Padilla et al.,2009). In the present analyses, theconductor of nephilids is treated ashomologous to the araneoid conductor,and character definitions and scorings inthe matrix for the conductor and the‘‘embolic conductor’’ are revised according-ly: character 144 coding the presence or ab-sence of ‘‘embolic conductor’’ is removedfrom the matrix and characters 145–151refer now to the conductor instead of the‘‘embolic conductor.’’ One additional statehas been added to character 148 (conductorcurvature) to describe the spirally curvedconductor in some tetragnathids—circularly curved, following the tegular margin. Inaddition, several errors in the srcinal ma-trix were corrected. Kuntner (2006) coded Nesticus  as lacking a conductor; however, aconductor is present in this genus (e.g.,Agnarsson, 2004; Griswold et al., 1998;Huber, 1993), and accordingly, we havecorrected the scoring for  Nesticus  to reflectit. Careful examination of the epigynumof   C. thisbe  suggests that the copulato-ry ducts open ventrally (Fig. 2E G) and notcaudally as suggested by Kuntner (2006).Our interpretation is also supported by SEM observations (Fig. 5D). As a result,the structures in  C. thisbe  referred toas ‘‘copulatory ducts’’ by Kuntner (2006: fig.25B, C) are actually the fertilizationducts and vice versa. The complete morpho-logical matrix used in the analyses is given inAppendix 1.In addition to the morphological char-acters, molecular data available in GenBank for many of the taxa were downloaded andused in the analyses. We have used se-quences from three nuclear (28S, 18S, andH3) and three mitochondrial genes (12S,16S, and COI). The accession numbers of the sequences used in the analyses aregiven in Appendix 2. Several terminalsare ‘‘composed’’ of two species:  Argiopeargentata  (Fabricius, 1775) is representedby   A. argentata  and  Argiope savignyi  Levi,1968 (as in A´ lvarez-Padilla et al., 2009); Clitaetra episinoides  Simon, 1889, by   C.episinoides  and  Clitaetra  sp. from SouthAfrica (as in A´ lvarez-Padilla et al., 2009).Although such ‘‘chimaeras’’ are not desir-able, the monophyly of neither  Argiope  nor Clitaetra  has been questioned; there-fore, any potential errors in phylogeneticinference caused by these composed termi-nals should be minimal.  Analyses . All data, morphological andmolecular, were analyzed simultaneously under the parsimony criterion. Becausepositional homology in ribosomal genesis not a trivial problem due to the presenceof insertion and deletions, we have investi-gated two different approaches to thisproblem. In the first case, we used thetraditional ‘‘static homology approximation’’ where, before the phylogenetic analysis, thehomologous gene fragments are aligned with a multiple sequence alignment algo-rithm. To generate the alignments, we haveused the program MAFFT v6 and the L-INS-I method (Katoh et al., 2002, 2005).Aligned gene fragments were combined with the morphological data and wereanalyzed with TNT v1.1 (Goloboff et al.,2003). Data were analyzed under both equaland implied weights (Goloboff, 1993), either with 1,000 replications, keeping 10 trees perreplication, or 500 replications, keeping 200trees per replication. In both cases, gaps were treated as missing data. Trees wereswapped by the TBR algorithm, andminimum length  5  0 (the default in TNT) was used as a collapsing rule in all search-es. Jackknife with 36% probability of char-acter removal and bootstrap support values with 1,000 pseudoreplications were cal-culated in TNT for the static align-ments. For the analyses under implied weights, we have sampled different  k  values within a wide range of variationallowed by TNT 1.1. Values from 1 to 100 were sampled; with denser sampling in thelower range (1–20) until topology convergedto the one from equal weights (see alsoDimitrov and Hormiga, 2009).One alternative approach to the problemof positional homology is direct optimiza-tion (Wheeler, 1996). Parsimony analyses 304  Bulletin of the Museum of Comparative Zoology, Vol. 159, No. 6  Figure 2.  Clitaetra thisbe   male: A, palp retrolateral; B, palp prolateral; C, palp ventral; D, palp schematic.  Clitaetra thisbe   female:E, vulva dorsal; F, epigynum ventral; G, schematic drawing of the female genitalia. Note the broken embolus.  Scale lines:   A, B, D,E, G 0.1 mm; C, F 0.2 mm. C LITAETRA  N  Dimitrov et al.  305
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