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Yong HS, Song SL, Chua KO, Wayan Suana I, Eamsobhana P, Tan J, Lim PE, Chan KG. Complete mitochondrial genomes and phylogenetic relationships of the genera Nephila and Trichonephila (Araneae, Araneoidea). Sci Rep 2021; 11:10680. [PMID: 34021208 PMCID: PMC8139964 DOI: 10.1038/s41598-021-90162-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/29/2021] [Indexed: 02/04/2023] Open
Abstract
Spiders of the genera Nephila and Trichonephila are large orb-weaving spiders. In view of the lack of study on the mitogenome of these genera, and the conflicting systematic status, we sequenced (by next generation sequencing) and annotated the complete mitogenomes of N. pilipes, T. antipodiana and T. vitiana (previously N. vitiana) to determine their features and phylogenetic relationship. Most of the tRNAs have aberrant clover-leaf secondary structure. Based on 13 protein-coding genes (PCGs) and 15 mitochondrial genes (13 PCGs and two rRNA genes), Nephila and Trichonephila form a clade distinctly separated from the other araneid subfamilies/genera. T. antipodiana forms a lineage with T. vitiana in the subclade containing also T. clavata, while N. pilipes forms a sister clade to Trichonephila. The taxon vitiana is therefore a member of the genus Trichonephila and not Nephila as currently recognized. Studies on the mitogenomes of other Nephila and Trichonephila species and related taxa are needed to provide a potentially more robust phylogeny and systematics.
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Affiliation(s)
- Hoi-Sen Yong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sze-Looi Song
- Institute for Advanced Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Institute of Ocean and Earth Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kah-Ooi Chua
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - I Wayan Suana
- Faculty of Science and Mathematics, Mataram University, Mataram, Indonesia
| | - Praphathip Eamsobhana
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Ji Tan
- Department of Agricultural and Food Science, Universiti Tunku Abdul Rahman, 31900, Kampar, Perak, Malaysia
| | - Phaik-Eem Lim
- Institute of Ocean and Earth Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Guangdong Provincial Key Laboratory of Marine Biology, Institute of Marine Sciences, Shantou University, Shantou, 515063, China
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Abel C, Schneider JM, Kuntner M, Harms D. Phylogeography of the ‘cosmopolitan’ orb-weaver Argiope trifasciata (Araneae: Araneidae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Few spider species show truly cosmopolitan distributions. Among them is the banded garden spider Argiope trifasciata, which is reported from six continents across major climatic gradients and geographical boundaries. In orb-weaver spiders, such global distributions might be a result of lively dispersal via ballooning. However, wide distributions might also be artefactual, owing to our limited understanding of species taxonomy. To test the hypothesis that A. trifasciata might be a complex of cryptic species with more limited geographical ranges, we investigated the biogeographical structure and evolutionary history of A. trifasciata through a combination of time-calibrated phylogenetic analyses (57 terminals and three genes), ancestral range reconstruction and species delimitation methods. Our results strongly suggest that A. trifasciata as currently defined is not a single species. Its populations fall into five reciprocally monophyletic clades that are genetically distinct and have evolutionary origins in the Plio-Pleistocene. These clades are confined to East Asia, temperate Australia, Hawaii, the New World and the Old World (Africa and most of the Palaearctic). Our results provide the basis for future investigation of morphological and/or ecological disparity between the populations that are likely to represent species, in addition to examinations of the attributes and dispersal modes of these species.
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Affiliation(s)
- Christoph Abel
- Zoological Museum, Center of Natural History, Universität Hamburg, Martin-Luther-King-Platz, Hamburg, Germany
- Institute of Zoology, Universität Hamburg, Martin-Luther-King-Platz, Hamburg, Germany
| | - Jutta M Schneider
- Institute of Zoology, Universität Hamburg, Martin-Luther-King-Platz, Hamburg, Germany
| | - Matjaž Kuntner
- Evolutionary Zoology Laboratory, Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot, Ljubljana, Slovenia
- Evolutionary Zoology Laboratory, Biological Institute ZRC SAZU, Novi trg, Ljubljana, Slovenia
| | - Danilo Harms
- Zoological Museum, Center of Natural History, Universität Hamburg, Martin-Luther-King-Platz, Hamburg, Germany
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Purchart L, Hula V, Fric ZF. Comparison of the biogeographic origin of three terrestrial arthropod groups in the Socotra Archipelago (Yemen). RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2020. [DOI: 10.1007/s12210-020-00926-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Magalhaes ILF, Azevedo GHF, Michalik P, Ramírez MJ. The fossil record of spiders revisited: implications for calibrating trees and evidence for a major faunal turnover since the Mesozoic. Biol Rev Camb Philos Soc 2020; 95:184-217. [PMID: 31713947 DOI: 10.1111/brv.12559] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 01/24/2023]
Abstract
Studies in evolutionary biology and biogeography increasingly rely on the estimation of dated phylogenetic trees using molecular clocks. In turn, the calibration of such clocks is critically dependent on external evidence (i.e. fossils) anchoring the ages of particular nodes to known absolute ages. In recent years, a plethora of new fossil spiders, especially from the Mesozoic, have been described, while the number of studies presenting dated spider phylogenies based on fossil calibrations increased sharply. We critically evaluate 44 of these studies, which collectively employed 67 unique fossils in 180 calibrations. Approximately 54% of these calibrations are problematic, particularly regarding unsupported assignment of fossils to extant clades (44%) and crown (rather than stem) dating (9%). Most of these cases result from an assumed equivalence between taxonomic placement of fossils and their phylogenetic position. To overcome this limitation, we extensively review the literature on fossil spiders, with a special focus on putative synapomorphies and the phylogenetic placement of fossil species with regard to their importance for calibrating higher taxa (families and above) in the spider tree of life. We provide a curated list including 41 key fossils intended to be a basis for future estimations of dated spider phylogenies. In a second step, we use a revised set of 23 calibrations to estimate a new dated spider tree of life based on transcriptomic data. The revised placement of key fossils and the new calibrated tree are used to resolve a long-standing debate in spider evolution - we tested whether there has been a major turnover in the spider fauna between the Mesozoic and Cenozoic. At least 17 (out of 117) extant families have been recorded from the Cretaceous, implying that at least 41 spider lineages in the family level or above crossed the Cretaeous-Paleogene (K-Pg) boundary. The putative phylogenetic affinities of families known only from the Mesozoic suggest that at least seven Cretaceous families appear to have no close living relatives and might represent extinct lineages. There is no unambiguous fossil evidence of the retrolateral tibial apophysis clade (RTA-clade) in the Mesozoic, although molecular clock analyses estimated the major lineages within this clade to be at least ∼100 million years old. Our review of the fossil record supports a major turnover showing that the spider faunas in the Mesozoic and the Cenozoic are very distinct at high taxonomic levels, with the Mesozoic dominated by Palpimanoidea and Synspermiata, while the Cenozoic is dominated by Araneoidea and RTA-clade spiders.
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Affiliation(s)
- Ivan L F Magalhaes
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
| | - Guilherme H F Azevedo
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
| | - Peter Michalik
- Zoologisches Institut und Museum, Universität Greifswald, Loitzer Straβe 26, Greifswald, D-17489, Germany
| | - Martín J Ramírez
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
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Kuntner M, Hamilton CA, Cheng RC, Gregorič M, Lupše N, Lokovšek T, Lemmon EM, Lemmon AR, Agnarsson I, Coddington JA, Bond JE. Golden Orbweavers Ignore Biological Rules: Phylogenomic and Comparative Analyses Unravel a Complex Evolution of Sexual Size Dimorphism. Syst Biol 2019; 68:555-572. [PMID: 30517732 PMCID: PMC6568015 DOI: 10.1093/sysbio/syy082] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/20/2018] [Accepted: 11/26/2018] [Indexed: 11/14/2022] Open
Abstract
Instances of sexual size dimorphism (SSD) provide the context for rigorous tests of biological rules of size evolution, such as Cope's rule (phyletic size increase), Rensch's rule (allometric patterns of male and female size), as well as male and female body size optima. In certain spider groups, such as the golden orbweavers (Nephilidae), extreme female-biased SSD (eSSD, female:male body length $\ge$2) is the norm. Nephilid genera construct webs of exaggerated proportions, which can be aerial, arboricolous, or intermediate (hybrid). First, we established the backbone phylogeny of Nephilidae using 367 anchored hybrid enrichment markers, then combined these data with classical markers for a reference species-level phylogeny. Second, we used the phylogeny to test Cope and Rensch's rules, sex specific size optima, and the coevolution of web size, type, and features with female and male body size and their ratio, SSD. Male, but not female, size increases significantly over time, and refutes Cope's rule. Allometric analyses reject the converse, Rensch's rule. Male and female body sizes are uncorrelated. Female size evolution is random, but males evolve toward an optimum size (3.2-4.9 mm). Overall, female body size correlates positively with absolute web size. However, intermediate sized females build the largest webs (of the hybrid type), giant female Nephila and Trichonephila build smaller webs (of the aerial type), and the smallest females build the smallest webs (of the arboricolous type). We propose taxonomic changes based on the criteria of clade age, monophyly and exclusivity, classification information content, and diagnosability. Spider families, as currently defined, tend to be between 37 million years old and 98 million years old, and Nephilidae is estimated at 133 Ma (97-146), thus deserving family status. We, therefore, resurrect the family Nephilidae Simon 1894 that contains Clitaetra Simon 1889, the Cretaceous GeratonephilaPoinar and Buckley (2012), Herennia Thorell 1877, IndoetraKuntner 2006, new rank, Nephila Leach 1815, Nephilengys L. Koch 1872, Nephilingis Kuntner 2013, Palaeonephila Wunderlich 2004 from Tertiary Baltic amber, and TrichonephilaDahl 1911, new rank. We propose the new clade Orbipurae to contain Araneidae Clerck 1757, Phonognathidae Simon 1894, new rank, and Nephilidae. Nephilid female gigantism is a phylogenetically ancient phenotype (over 100 Ma), as is eSSD, though their magnitudes vary by lineage.
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Affiliation(s)
- Matjaž Kuntner
- Evolutionary Zoology Laboratory, Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia
- Evolutionary Zoology Laboratory, Biological Institute ZRC SAZU, Novi trg 2, SI-1001 Ljubljana, Slovenia
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution, NW, Washington, DC 20560-0105, USA
- Centre for Behavioural Ecology and Evolution, College of Life Sciences, Hubei University, 368 Youyi Road, Wuhan, Hubei 430062, China
| | - Chris A Hamilton
- Department of Entomology, Plant Pathology, & Nematology, University of Idaho, 875 Perimeter Dr. MS 2329, Moscow, ID 83844-2329, USA
| | - Ren-Chung Cheng
- Evolutionary Zoology Laboratory, Biological Institute ZRC SAZU, Novi trg 2, SI-1001 Ljubljana, Slovenia
- Department of Life Sciences, National Chung Hsing University, No.145 Xingda Rd., South Dist., Taichung City 402, Taiwan
| | - Matjaž Gregorič
- Evolutionary Zoology Laboratory, Biological Institute ZRC SAZU, Novi trg 2, SI-1001 Ljubljana, Slovenia
| | - Nik Lupše
- Evolutionary Zoology Laboratory, Biological Institute ZRC SAZU, Novi trg 2, SI-1001 Ljubljana, Slovenia
- Division of Animal Evolutionary Biology, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Tjaša Lokovšek
- Evolutionary Zoology Laboratory, Biological Institute ZRC SAZU, Novi trg 2, SI-1001 Ljubljana, Slovenia
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL 32306-4295, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL 32306-4120, USA
| | - Ingi Agnarsson
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution, NW, Washington, DC 20560-0105, USA
- Department of Biology, University of Vermont, 316 Marsh Life Science Building, 109 Carrigan Drive, Burlington, VT 05405-0086, USA
| | - Jonathan A Coddington
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution, NW, Washington, DC 20560-0105, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California Davis, 1 Shields Drive, Davis, CA 95616, USA
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Ballesteros JA, Hormiga G. Species delimitation of the North American orchard-spider Leucauge venusta (Walckenaer, 1841) (Araneae, Tetragnathidae). Mol Phylogenet Evol 2018; 121:183-197. [PMID: 29337274 DOI: 10.1016/j.ympev.2018.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 12/17/2022]
Abstract
The orchard spider, Leucauge venusta (Walckenaer, 1841) is one of the most common and abundant orb-weavers in North America. This species has a broad geographic distribution extending across tropical and temperate regions of the Americas from Canada to Brazil. Guided by a preliminary observation of the barcode gap between sequences from specimens of L. venusta collected in Florida and other North American localities, we collected across a transect through the southeastern USA to investigate the observed genetic divide. The dataset, complemented with additional samples from Mexico, and Brazil was analyzed for species delimitation using STACEY and bGMYC based on sequences from one nuclear (ITS2) and one mitochondrial marker (COI). The analyses clearly separate USA samples into two deeply divergent and geographically structured groups (north-south) which we interpret as two different species. We generated ecological niche models for these two groups rejecting a niche equivalence hypothesis for these lineages. Taxonomic changes are proposed based on these findings, Leucauge venusta is restricted to denote the northern clade, and its known distribution restricted to the USA. Leucauge argyrobapta (White, 1841) is removed from synonymy to denote the populations in Florida, Mexico and Brazil. Although the delimitation analyses suggest each of these geographic clusters within the L. argyrobapta samples represent different species, more specimens from Central and South America are needed to properly test the cohesion of L. argyrobapta populations.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Biological Sciences, The George Washington University, 2029 G Street NW, Bell Hall 302, Washington, DC 20052, United States; Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, United States.
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G Street NW, Bell Hall 302, Washington, DC 20052, United States
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Low VL, Norma-Rashid Y, Ubaidillah R, Yusoff A, Prakash BK, Tan TK, Chen CD, Sofian-Azirun M. Does colour matter? Genetic differentiation of colour morphs of the Asian golden web spider Nephila antipodiana (Araneae: Nephilidae). ANIM BIOL 2018. [DOI: 10.1163/15707563-18000002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Here we present the first attempt to test for genetic differentiation among four distinct colour morphs of the Asian golden web spider Nephila antipodiana Walckenaer. Fragments of the 18S rRNA (18S) and cytochrome c oxidase subunit I (COI) genes were sequenced in eight populations of N. antipodiana belonging to four distinct colour morphs: yellow, yellowish green, and two newly discovered morphs, reddish yellow and white-spotted. The nuclear sequences amplified from females of the four colour morphs were identical. The mitochondrial COI sequences, on the other hand, revealed slightly higher variation by recovering three haplotypes belonging to two different clades. Clade I comprises yellow, yellowish green and reddish yellow morphs from the mainland of Southeast Asia and Java, whereas clade II is restricted to white-spotted morph originating from Borneo. The low genetic divergence between both clades, despite being distinctive, undoubtedly provides new insight into the genetic diversity of this polymorphic species.
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Affiliation(s)
- Van Lun Low
- 1Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, Kuala Lumpur, Malaysia
| | - Yusoff Norma-Rashid
- 2Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- 3Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Rosichon Ubaidillah
- 4Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Bogor, Indonesia
| | - Amri Yusoff
- 5Faculty of Arts, Computing and Creative Industry, Sultan Idris Education University, Tanjung Malim, Perak, Malaysia
| | - Batah Kunalan Prakash
- 2Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Tiong Kai Tan
- 6Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chee Dhang Chen
- 2Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Sofian-Azirun
- 2Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
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Tan J, Chan ZY, Lim PE, Koh JKH, Yong HS. A multigene approach to determine the molecular phylogeography of Argiope mangal and Argiope dang (Araneae: Araneidae) and their genetic relationships with the Argiope aetherea species group. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Toussaint EFA, Condamine FL. To what extent do new fossil discoveries change our understanding of clade evolution? A cautionary tale from burying beetles (Coleoptera:Nicrophorus). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12710] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Emmanuel F. A. Toussaint
- Department of Ecology & Evolutionary Biology & Division of Entomology; Biodiversity Institute; University of Kansas; Lawrence KS 66045 USA
| | - Fabien L. Condamine
- Department of Biological Sciences; University of Alberta; Edmonton AB T6G 2E9 Canada
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Hoebeke ER, Huffmaster W, Freeman BJ. Nephila clavata L Koch, the Joro Spider of East Asia, newly recorded from North America (Araneae: Nephilidae). PeerJ 2015; 3:e763. [PMID: 25699210 PMCID: PMC4327315 DOI: 10.7717/peerj.763] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 01/22/2015] [Indexed: 11/20/2022] Open
Abstract
Nephila clavata L Koch, known as the Joro spider and native to East Asia (Japan, China, Korea, and Taiwan), is newly reported from North America. Specimens from several locations in northeast Georgia were collected from around residential properties in Barrow, Jackson, and Madison counties in late October and early November 2014. These are the first confirmed records of the species in the New World. Our collections, along with confirmed images provided by private citizens, suggest that the Joro spider is established in northeast Georgia. Genomic sequence data for the COI gene obtained from two specimens conforms to published sequences for N. clavata, providing additional confirmation of species identity. Known collection records are listed and mapped using geocoding. Our observations are summarized along with published background information on biology in Asia and we hypothesize on the invasion history and mode of introduction into North America. Recognition features are given and photographic images of the male and female are provided to aid in their differentiation from the one native species of the genus (Nephila clavipes) in North America.
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Affiliation(s)
- E. Richard Hoebeke
- Georgia Museum of Natural History and Department of Entomology, University of Georgia, Athens, GA, USA
| | | | - Byron J. Freeman
- Georgia Museum of Natural History and Eugene P. Odum School of Ecology, University of Georgia, Athens, GA, USA
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Lee VMJ, Kuntner M, Li D. Ballooning behavior in the golden orbweb spider Nephila pilipes (Araneae: Nephilidae). Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Pan WJ, Fang HY, Zhang P, Pan HC. The complete mitochondrial genome of Nephila clavata (Araneae: Nephilidae) Chinese population. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:994-5. [PMID: 24938104 DOI: 10.3109/19401736.2014.926521] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Nephila clavata is a circular molecule of 14,433 bp in length, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The A + T content of the overall base composition of H-strand is 76.1% (T: 40.0%; C: 9.2%; A: 36.1%; G: 14.7%). COI gene begins with TTA as start codon, COII gene begins with TTT as start codon, COIII gene begins with TTG as start codon, ND3, ND4L, ND6 and ATP8 genes begin with ATT as start codon, while other six protein-coding genes start with ATA as initiation codon. ND3, ND4, ND4L, ND5, COI, COII, ATP6 and ATP8 genes are terminated with TAA as stop codon, ND1, ND2, ND6 and Cyt b end with TAG, and COIII ends with TGA.
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Affiliation(s)
- Wen-Jian Pan
- a Laboratory of Molecular Evolution and Biodiversity , College of Life Sciences, Anhui Normal University , Wuhu , P. R. China
| | - Hong-Yan Fang
- a Laboratory of Molecular Evolution and Biodiversity , College of Life Sciences, Anhui Normal University , Wuhu , P. R. China
| | - Peng Zhang
- a Laboratory of Molecular Evolution and Biodiversity , College of Life Sciences, Anhui Normal University , Wuhu , P. R. China
| | - Hong-Chun Pan
- a Laboratory of Molecular Evolution and Biodiversity , College of Life Sciences, Anhui Normal University , Wuhu , P. R. China
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Chaw RC, Zhao Y, Wei J, Ayoub NA, Allen R, Atrushi K, Hayashi CY. Intragenic homogenization and multiple copies of prey-wrapping silk genes in Argiope garden spiders. BMC Evol Biol 2014; 14:31. [PMID: 24552485 PMCID: PMC3933166 DOI: 10.1186/1471-2148-14-31] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 02/14/2014] [Indexed: 11/15/2022] Open
Abstract
Background Spider silks are spectacular examples of phenotypic diversity arising from adaptive molecular evolution. An individual spider can produce an array of specialized silks, with the majority of constituent silk proteins encoded by members of the spidroin gene family. Spidroins are dominated by tandem repeats flanked by short, non-repetitive N- and C-terminal coding regions. The remarkable mechanical properties of spider silks have been largely attributed to the repeat sequences. However, the molecular evolutionary processes acting on spidroin terminal and repetitive regions remain unclear due to a paucity of complete gene sequences and sampling of genetic variation among individuals. To better understand spider silk evolution, we characterize a complete aciniform spidroin gene from an Argiope orb-weaving spider and survey aciniform gene fragments from congeneric individuals. Results We present the complete aciniform spidroin (AcSp1) gene from the silver garden spider Argiope argentata (Aar_AcSp1), and document multiple AcSp1 loci in individual genomes of A. argentata and the congeneric A. trifasciata and A. aurantia. We find that Aar_AcSp1 repeats have >98% pairwise nucleotide identity. By comparing AcSp1 repeat amino acid sequences between Argiope species and with other genera, we identify regions of conservation over vast amounts of evolutionary time. Through a PCR survey of individual A. argentata, A. trifasciata, and A. aurantia genomes, we ascertain that AcSp1 repeats show limited variation between species whereas terminal regions are more divergent. We also find that average dN/dS across codons in the N-terminal, repetitive, and C-terminal encoding regions indicate purifying selection that is strongest in the N-terminal region. Conclusions Using the complete A. argentata AcSp1 gene and spidroin genetic variation between individuals, this study clarifies some of the molecular evolutionary processes underlying the spectacular mechanical attributes of aciniform silk. It is likely that intragenic concerted evolution and functional constraints on A. argentata AcSp1 repeats result in extreme repeat homogeneity. The maintenance of multiple AcSp1 encoding loci in Argiope genomes supports the hypothesis that Argiope spiders require rapid and efficient protein production to support their prolific use of aciniform silk for prey-wrapping and web-decorating. In addition, multiple gene copies may represent the early stages of spidroin diversification.
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Affiliation(s)
- R Crystal Chaw
- Department of Biology, University of California, 900 University Avenue, Riverside 92507, Riverside, CA, USA.
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Kuntner M, Arnedo MA, Trontelj P, Lokovšek T, Agnarsson I. A molecular phylogeny of nephilid spiders: evolutionary history of a model lineage. Mol Phylogenet Evol 2013; 69:961-79. [PMID: 23811436 DOI: 10.1016/j.ympev.2013.06.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/25/2013] [Accepted: 06/15/2013] [Indexed: 11/29/2022]
Abstract
The pantropical orb web spider family Nephilidae is known for the most extreme sexual size dimorphism among terrestrial animals. Numerous studies have made Nephilidae, particularly Nephila, a model lineage in evolutionary research. However, a poorly understood phylogeny of this lineage, relying only on morphology, has prevented thorough evolutionary syntheses of nephilid biology. We here use three nuclear and five mitochondrial genes for 28 out of 40 nephilid species to provide a more robust nephilid phylogeny and infer clade ages in a fossil-calibrated Bayesian framework. We complement the molecular analyses with total evidence analysis including morphology. All analyses find strong support for nephilid monophyly and exclusivity and the monophyly of the genera Herennia and Clitaetra. The inferred phylogenetic structure within Nephilidae is novel and conflicts with morphological phylogeny and traditional taxonomy. Nephilengys species fall into two clades, one with Australasian species (true Nephilengys) as sister to Herennia, and another with Afrotropical species (Nephilingis Kuntner new genus) as sister to a clade containing Clitaetra plus most currently described Nephila. Surprisingly, Nephila is also diphyletic, with true Nephila containing N. pilipes+N. constricta, and the second clade with all other species sister to Clitaetra; this "Nephila" clade is further split into an Australasian clade that also contains the South American N. sexpunctata and the Eurasian N. clavata, and an African clade that also contains the Panamerican N. clavipes. An approximately unbiased test constraining the monophyly of Nephilengys, Nephila, and Nephilinae (Nephila, Nephilengys, Herennia), respectively, rejected Nephilengys monophyly, but not that of Nephila and Nephilinae. Further data are therefore necessary to robustly test these two new, but inconclusive findings, and also to further test the precise placement of Nephilidae within the Araneoidea. For divergence date estimation we set the minimum bound for the stems of Nephilidae at 40 Ma and of Nephila at 16 Ma to accommodate Palaeonephila from Baltic amber and Dominican Nephila species, respectively. We also calibrated and dated the phylogeny under three different interpretations of the enigmatic 165 Ma fossil Nephila jurassica, which we suspected based on morphology to be misplaced. We found that by treating N. jurassica as stem Nephila or nephilid the inferred clade ages were vastly older, and the mitochondrial substitution rates much slower than expected from other empirical spider data. This suggests that N. jurassica is not a Nephila nor a nephilid, but possibly a stem orbicularian. The estimated nephilid ancestral age (40-60 Ma) rejects a Gondwanan origin of the family as most of the southern continents were already split at that time. The origin of the family is equally likely to be African, Asian, or Australasian, with a global biogeographic history dominated by dispersal events. A reinterpretation of web architecture evolution suggests that a partially arboricolous, asymmetric orb web with a retreat, as exemplified by both groups of "Nephilengys", is plesiomorphic in Nephilidae, that this architecture was modified into specialized arboricolous webs in Herennia and independently in Clitaetra, and that the web became aerial, gigantic, and golden independently in both "Nephila" groups. The new topology questions previously hypothesized gradual evolution of female size from small to large, and rather suggests a more mosaic evolutionary pattern with independent female size increases from medium to giant in both "Nephila" clades, and two reversals back to medium and small; combined with male size evolution, this pattern will help detect gross evolutionary events leading to extreme sexual size dimorphism, and its morphological and behavioral correlates.
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Affiliation(s)
- Matjaž Kuntner
- Institute of Biology, Scientific Research Centre, Slovenian Academy of Sciences and Arts, Ljubljana, Slovenia; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; College of Life Sciences, Hubei University, Wuhan 430062, Hubei, China.
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Danielson-François A, Hou C, Cole N, Tso IM. Scramble competition for moulting females as a driving force for extreme male dwarfism in spiders. Anim Behav 2012. [DOI: 10.1016/j.anbehav.2012.07.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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BLAMIRES SEANJ, WU CHUNLIN, BLACKLEDGE TODDA, TSO IMIN. Environmentally induced post-spin property changes in spider silks: influences of web type, spidroin composition and ecology. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01884.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Schneider JM, Michalik P. One-shot genitalia are not an evolutionary dead end - regained male polygamy in a sperm limited spider species. BMC Evol Biol 2011; 11:197. [PMID: 21740561 PMCID: PMC3145602 DOI: 10.1186/1471-2148-11-197] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 07/08/2011] [Indexed: 11/24/2022] Open
Abstract
Background Monogynous mating systems with extremely low male mating rates have several independent evolutionary origins and are associated with drastic adaptations involving self-sacrifice, one-shot genitalia, genital damage, and termination of spermatogenesis immediately after maturation. The combination of such extreme traits likely restricts evolutionary potential perhaps up to the point of making low male mating rates irreversible and hence may constitute an evolutionary dead end. Here, we explore the case of a reversion to multiple mating from monogynous ancestry in golden orb-web spiders, Nephila senegalensis. Results Male multiple mating is regained by the loss of genital damage and sexual cannibalism but spermatogenesis is terminated with maturation, restricting males to a single loading of their secondary mating organs and a fixed supply of sperm. However, males re-use their mating organs and by experimentally mating males to many females, we show that the sperm supply is divided between copulations without reloading the pedipalps. Conclusion By portioning their precious sperm supply, males achieve an average mating rate of four females which effectively doubles the maximal mating rate of their ancestors. A heritage of one-shot genitalia does not completely restrict the potential to increase mating rates in Nephila although an upper limit is defined by the available sperm load. Future studies should now investigate how males use this potential in the field and identify selection pressures responsible for a reversal from monogynous to polygynous mating strategies.
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Affiliation(s)
- Jutta M Schneider
- Biozentrum Grindel, Zoological Institute and Museum, University of Hamburg, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany.
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Kuntner M, Agnarsson I. Phylogeography of a successful aerial disperser: the golden orb spider Nephila on Indian Ocean islands. BMC Evol Biol 2011; 11:119. [PMID: 21554687 PMCID: PMC3098804 DOI: 10.1186/1471-2148-11-119] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 05/09/2011] [Indexed: 11/10/2022] Open
Abstract
Background The origin and diversification patterns of lineages across the Indian Ocean islands are varied due to the interplay of the complex geographic and geologic island histories, the varying dispersal abilities of biotas, and the proximity to major continental landmasses. Our aim was to reconstruct phylogeographic history of the giant orbweaving spider (Nephila) on western Indian Ocean islands (Madagascar, Mayotte, Réunion, Mauritius, Rodrigues), to test its origin and route of dispersal, and to examine the consequences of good dispersal abilities for colonization and diversification, in comparison with related spiders (Nephilengys) inhabiting the same islands, and with other organisms known for over water dispersal. We used mitochondrial (COI) and nuclear (ITS2) markers to examine phylogenetic and population genetic patterns in Nephila populations and species. We employed Bayesian and parsimony methods to reconstruct phylogenies and haplotype networks, respectively, and calculated genetic distances, fixation indices, and estimated clade ages under a relaxed clock model. Results Our results suggest an African origin of Madagascar Nephila inaurata populations via Cenozoic dispersal, and the colonization of the Mascarene islands from Madagascar. We find evidence of gene flow across Madagascar and Comoros. The Mascarene islands share a common 'ancestral' COI haplotype closely related to those found on Madagascar, but itself absent, or as yet unsampled, from Madagascar. Each island has one or more unique haplotypes related to the ancestral Mascarene haplotype. The Indian Ocean N. inaurata are genetically distinct from the African populations. Conclusions Nephila spiders colonized Madagascar from Africa about 2.5 (0.6-5.3) Ma. Our results are consistent with subsequent, recent and rapid, colonization of all three Mascarene islands. On each island, however, we detected unique haplotypes, consistent with a limited gene flow among the islands subsequent to colonization, a scenario that might be referred to as speciation in progress. However, due to relatively small sample sizes, we cannot rule out that we simply failed to collect Mascarene haplotypes on Madagascar, a scenario that might imply human mediated dispersal. Nonetheless, the former interpretation better fits the available data and results in a pattern similar to the related Nephilengys. Nephilengys, however, shows higher genetic divergences with diversification on more remote islands. That the better disperser of the two lineages, Nephila, has colonized more islands but failed to diversify, demonstrates how dispersal ability can shape both the patterns of colonization and formation of species across archipelagos.
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Affiliation(s)
- Matjaž Kuntner
- Institute of Biology, Scientific Research Centre, Slovenian Academy of Sciences and Arts, Ljubljana, Slovenia.
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Selden PA, Shih C, Ren D. A golden orb-weaver spider (Araneae: Nephilidae: Nephila) from the Middle Jurassic of China. Biol Lett 2011; 7:775-8. [PMID: 21508021 PMCID: PMC3169061 DOI: 10.1098/rsbl.2011.0228] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nephila are large, conspicuous weavers of orb webs composed of golden silk, in tropical and subtropical regions. Nephilids have a sparse fossil record, the oldest described hitherto being Cretaraneus vilaltae from the Cretaceous of Spain. Five species from Neogene Dominican amber and one from the Eocene of Florissant, CO, USA, have been referred to the extant genus Nephila. Here, we report the largest known fossil spider, Nephila jurassica sp. nov., from Middle Jurassic (approx. 165 Ma) strata of Daohugou, Inner Mongolia, China. The new species extends the fossil record of the family by approximately 35 Ma and of the genus Nephila by approximately 130 Ma, making it the longest ranging spider genus known. Nephilidae originated somewhere on Pangaea, possibly the North China block, followed by dispersal almost worldwide before the break-up of the supercontinent later in the Mesozoic. The find suggests that the palaeoclimate was warm and humid at this time. This giant fossil orb-weaver provides evidence of predation on medium to large insects, well known from the Daohugou beds, and would have played an important role in the evolution of these insects.
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Affiliation(s)
- Paul A Selden
- College of Life Sciences, Capital Normal University, Beijing 100048, People's Republic of China
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