51
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Wolff JO, Paterno GB, Liprandi D, Ramírez MJ, Bosia F, Meijden A, Michalik P, Smith HM, Jones BR, Ravelo AM, Pugno N, Herberstein ME. Evolution of aerial spider webs coincided with repeated structural optimization of silk anchorages. Evolution 2019; 73:2122-2134. [DOI: 10.1111/evo.13834] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/11/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Jonas O. Wolff
- Department of Biological SciencesMacquarie University Sydney New South Wales 2109 Australia
| | - Gustavo B. Paterno
- Departamento de Ecologia, Centro de BiociênciasUniversidade Federal do Rio Grande do Norte (UFRN) Lagoa Nova 59072–970 Natal Rio Grande do Norte Brazil
- Instituto de Ciências Biológicas, Programa de Pós‐Graduação em EcologiaUniversidade Federal de Juiz de Fora Rua José Lourenço Kelmer 36036–900 Juiz de Fora Minas Gerais Brazil
| | - Daniele Liprandi
- Laboratory of Bio‐Inspired and Graphene Nanomechanics, Department of CivilEnvironmental and Mechanical EngineeringUniversity of Trento Via Masiano 77 I‐38123 Trento Italy
| | - Martín J. Ramírez
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Av. Ángel Gallardo 470 C1405DJR Buenos Aires Argentina
| | - Federico Bosia
- Department of Physics and Nanostructured Interfaces and Surfaces Interdepartmental CentreUniversità di Torino Via P. Giuria 1 10125 Torino Italy
| | - Arie Meijden
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIOUniversidade do Porto Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão, Vila do Conde Porto 4485–661 Portugal
| | - Peter Michalik
- Zoologisches Institut und MuseumUniversität Greifswald Loitzer Str. 26 17489 Greifswald Germany
| | - Helen M. Smith
- Australian Museum 1 William St Sydney New South Wales 2010 Australia
| | - Braxton R. Jones
- Department of Biological SciencesMacquarie University Sydney New South Wales 2109 Australia
| | - Alexandra M. Ravelo
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Av. Ángel Gallardo 470 C1405DJR Buenos Aires Argentina
| | - Nicola Pugno
- Laboratory of Bio‐Inspired and Graphene Nanomechanics, Department of CivilEnvironmental and Mechanical EngineeringUniversity of Trento Via Masiano 77 I‐38123 Trento Italy
- School of Engineering and Materials ScienceQueen Mary University Mile End Rd London E1 4NS UK
- KET Labs, Edoardo Amaldi Foundation Via del Politecnico snc 00133 Rome Italy
| | - Marie E. Herberstein
- Department of Biological SciencesMacquarie University Sydney New South Wales 2109 Australia
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Lüddecke T, Vilcinskas A, Lemke S. Phylogeny-Guided Selection of Priority Groups for Venom Bioprospecting: Harvesting Toxin Sequences in Tarantulas as a Case Study. Toxins (Basel) 2019; 11:E488. [PMID: 31450685 PMCID: PMC6784122 DOI: 10.3390/toxins11090488] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 12/24/2022] Open
Abstract
Animal venoms are promising sources of novel drug leads, but their translational potential is hampered by the low success rate of earlier biodiscovery programs, in part reflecting the narrow selection of targets for investigation. To increase the number of lead candidates, here we discuss a phylogeny-guided approach for the rational selection of venomous taxa, using tarantulas (family Theraphosidae) as a case study. We found that previous biodiscovery programs have prioritized the three subfamilies Ornithoctoninae, Selenocosmiinae, and Theraphosinae, which provide almost all of the toxin sequences currently available in public databases. The remaining subfamilies are poorly represented, if at all. These overlooked subfamilies include several that form entire clades of the theraphosid life tree, such as the subfamilies Eumenophorinae, Harpactirinae, and Stromatopelminae, indicating that biodiversity space has not been covered effectively for venom biodiscovery in Theraphosidae. Focusing on these underrepresented taxa will increase the likelihood that promising candidates with novel structures and mechanisms of action can be identified in future bioprospecting programs.
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Affiliation(s)
- Tim Lüddecke
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Winchesterstr. 2, 35394 Gießen, Germany.
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Winchesterstr. 2, 35394 Gießen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Sarah Lemke
- Institute for Insect Biotechnology, Justus-Liebig-University of Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
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53
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Michalik P, Kallal R, Dederichs TM, Labarque FM, Hormiga G, Giribet G, Ramírez MJ. Phylogenomics and genital morphology of cave raptor spiders (Araneae, Trogloraptoridae) reveal an independent origin of a flow‐through female genital system. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Peter Michalik
- Zoologisches Institut und Museum Universität Greifswald Greifswald Germany
| | - Robert Kallal
- Department of Biological Sciences The George Washington University Washington District of Columbia
| | - Tim M. Dederichs
- Zoologisches Institut und Museum Universität Greifswald Greifswald Germany
| | - Facundo M. Labarque
- Departamento de Ecologia e Biologia Evolutiva Universidade Federal de São Carlos São Carlos Brazil
| | - Gustavo Hormiga
- Department of Biological Sciences The George Washington University Washington District of Columbia
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts
| | - Martín J. Ramírez
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” – CONICET Buenos Aires Argentina
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54
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Feng C, Miller JA, Lin Y, Shu Y. Further study of two Chinese cave spiders (Araneae, Mysmenidae), with description of a new genus. Zookeys 2019; 870:77-100. [PMID: 31423079 PMCID: PMC6694075 DOI: 10.3897/zookeys.870.35971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/09/2019] [Indexed: 01/23/2023] Open
Abstract
The current paper expands knowledge of two Chinese cave spider species originally described in the genus Maymena Gertsch, 1960: M. paquini Miller, Griswold & Yin, 2009 and M. kehen Miller, Griswold & Yin, 2009. With the exception of these two species, the genus Maymena is endemic to the western hemisphere, and new evidence presented here supports the creation of a new genus for the Chinese species, which we name Yamaneta gen. nov. The male of Y. kehen is described for the first time. Detailed illustrations of the habitus, male palps and epigyne are provided for these two species, as well as descriptions of their webs. DNA sequences are provided for both Yamaneta species. We build on a previously published phylogenetic analysis of Mysmenidae to assess the phylogenetic position of Yamaneta and its relationship to true Maymena.
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Affiliation(s)
- Chengcheng Feng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, ChinaSichuan UniversitySichuanChina
| | - Jeremy A. Miller
- Department of Biodiversity Discovery, Naturalis Biodiversity Center, Postbus 9517 2300 RA Leiden, The NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
| | - Yucheng Lin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, ChinaSichuan UniversitySichuanChina
| | - Yunfei Shu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, ChinaSichuan UniversitySichuanChina
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55
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Zhan Y, Jiang H, Wu Q, Zhang H, Bai Z, Kuntner M, Tu L. Comparative morphology refines the conventional model of spider reproduction. PLoS One 2019; 14:e0218486. [PMID: 31276510 PMCID: PMC6611574 DOI: 10.1371/journal.pone.0218486] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 06/03/2019] [Indexed: 11/19/2022] Open
Abstract
Our understanding of spider reproductive biology is hampered by the vast anatomical diversity and difficulties associated with its study. Although authors agree on the two general types of female spider genitalia, haplogyne (plesiomorphic) and entelegyne (apomorphic), our understanding of variation within each group mostly concerns the external genital part, while the internal connections with the reproductive duct are largely unknown. Conventionally and simplistically, the spermathecae of haplogynes have simple two-way ducts, and those of entelegynes have separate copulatory and fertilization ducts for sperm to be transferred in and out of spermathecae, respectively. Sperm is discharged from the spermathecae directly into the uterus externus (a distal extension of the oviduct), which, commonly thought as homologous in both groups, is the purported location of internal fertilization in spiders. However, the structural evolution from haplo- to entelegyny remains unresolved, and thus the precise fertilization site in entelegynes is ambiguous. We aim to clarify this anatomical problem through a widely comparative morphological study of internal female genital system in entelegynes. Our survey of 147 epigyna (121 examined species in 97 genera, 34 families) surprisingly finds no direct connection between the fertilization ducts and the uterus externus, which, based on the homology with basal-most spider lineages, is a dead-end caecum in entelegynes. Instead, fertilization ducts usually connect with a secondary uterus externus, a novel feature taking over the functional role of the plesiomorphic uterus externus. We hypothesize that the transition from haplo- to entelegyny entailed not only the emergence of the two separate duct systems (copulatory, fertilization), but also involved substantial morphological changes in the distal part of the oviduct. Thus, the common oviduct may have shifted its distal connection from the uterus externus to the secondary uterus externus, perhaps facilitating discharge of larger eggs. Our findings suggest that the conventional model of entelegyne reproduction needs redefinition.
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Affiliation(s)
- Yongjia Zhan
- College of Life Sciences, Capital Normal University, Beijing, P. R. China
| | - He Jiang
- College of Life Sciences, Capital Normal University, Beijing, P. R. China
| | - Qingqing Wu
- Lang Yue Campus of Beijing 12th High School, Beijing, P. R. China
| | - Huitao Zhang
- Beijing Advanced Innovation Center for Imaging Technology, Capital Normal University, Beijing, P. R. China
| | - Zishang Bai
- College of Life Sciences, China Agricultural University, Beijing, P. R. China
| | - Matjaž Kuntner
- Evolutionary Zoology Laboratory, Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
- Evolutionary Zoology Laboratory, Biological Institute ZRC SAZU, Ljubljana, Slovenia
| | - Lihong Tu
- College of Life Sciences, Capital Normal University, Beijing, P. R. China
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56
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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: 61] [Impact Index Per Article: 12.2] [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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57
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Tamura K, Tao Q, Kumar S. Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates. Mol Biol Evol 2019; 35:1770-1782. [PMID: 29893954 PMCID: PMC5995221 DOI: 10.1093/molbev/msy044] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It shows excellent performance in estimating divergence times for both simulated and empirical molecular sequence data sets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of data sets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between evolutionary lineages and their respective descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits.
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Affiliation(s)
- Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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58
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Toward Spider Glue: Long Read Scaffolding for Extreme Length and Repetitious Silk Family Genes AgSp1 and AgSp2 with Insights into Functional Adaptation. G3-GENES GENOMES GENETICS 2019; 9:1909-1919. [PMID: 30975702 PMCID: PMC6553539 DOI: 10.1534/g3.119.400065] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An individual orb weaving spider can spin up to seven different types of silk, each with unique functions and material properties. The capture spiral silk of classic two-dimensional aerial orb webs is coated with an amorphous glue that functions to retain prey that get caught in a web. This unique modified silk is partially comprised of spidroins (spider fibroins) encoded by two members of the silk gene family. The glue differs from solid silk fibers as it is a viscoelastic, amorphic, wet material that is responsive to environmental conditions. Most spidroins are encoded by extremely large, highly repetitive genes that cannot be sequenced using short read technology alone, as the repetitive regions are longer than read length. We sequenced for the first time the complete genomic Aggregate Spidroin 1 (AgSp1) and Aggregate Spidroin 2 (AgSp2) glue genes of orb weaving spider Argiope trifasciata using error-prone long reads to scaffold for high accuracy short reads. The massive coding sequences are 42,270 bp (AgSp1) and 20,526 bp (AgSp2) in length, the largest silk genes currently described. The majority of the predicted amino acid sequence of AgSp1 consists of two similar but distinct motifs that are repeated ∼40 times each, while AgSp2 contains ∼48 repetitions of an AgSp1-similar motif, interspersed by regions high in glutamine. Comparisons of AgSp repetitive motifs from orb web and cobweb spiders show regions of strict conservation followed by striking diversification. Glues from these two spider families have evolved contrasting material properties in adhesion (stickiness), extensibility (stretchiness), and elasticity (the ability of the material to resume its native shape), which we link to mechanisms established for related silk genes in the same family. Full-length aggregate spidroin sequences from diverse species with differing material characteristics will provide insights for designing tunable bio-inspired adhesives for a variety of unique purposes.
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59
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Skelly J, Pushparajan C, Duncan EJ, Dearden PK. Evolution of the Torso activation cassette, a pathway required for terminal patterning and moulting. INSECT MOLECULAR BIOLOGY 2019; 28:392-408. [PMID: 30548465 DOI: 10.1111/imb.12560] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Embryonic terminal patterning and moulting are critical developmental processes in insects. In Drosophila and Tribolium both of these processes are regulated by the Torso-activation cassette (TAC). The TAC consists of a common receptor, Torso, ligands Trunk and prothoracicotropic hormone (PTTH), and the spatially restricted protein Torso-like, with combinations of these elements acting mechanistically to activate the receptor in different developmental contexts. In order to trace the evolutionary history of the TAC we determined the presence or absence of TAC components in the genomes of arthropods. Our analyses reveal that Torso, Trunk and PTTH are evolutionarily labile components of the TAC with multiple individual or combined losses occurring in the arthropod lineages leading to and within the insects. These losses are often correlated, with both ligands and receptor missing from the genome of the same species. We determine that the PTTH gene evolved in the common ancestor of Hemiptera and Holometabola, and is missing from the genomes of a number of species with experimentally demonstrated PTTH activity, implying another molecule may be involved in ecdysis in these species. In contrast, the torso-like gene is a common component of pancrustacean genomes.
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Affiliation(s)
- J Skelly
- Laboratory for Evolution and Development, Genomics Aotearoa, Biochemistry Department, University of Otago, Dunedin, Aotearoa-New Zealand
| | - C Pushparajan
- Laboratory for Evolution and Development, Genomics Aotearoa, Biochemistry Department, University of Otago, Dunedin, Aotearoa-New Zealand
| | - E J Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - P K Dearden
- Laboratory for Evolution and Development, Genomics Aotearoa, Biochemistry Department, University of Otago, Dunedin, Aotearoa-New Zealand
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60
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Mortimer B. A Spider’s Vibration Landscape: Adaptations to Promote Vibrational Information Transfer in Orb Webs. Integr Comp Biol 2019; 59:1636-1645. [DOI: 10.1093/icb/icz043] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Abstract
Spider orb webs are used not only for catching prey, but also for transmitting vibrational information to the spider. Vibrational information propagates from biological sources, such as potential prey or mates, but also abiotic sources, such as wind. Like other animals, the spider must cope with physical constraints acting on the propagation of vibrational information along surfaces and through materials—including loss of energy, distortion, and filtering. The spider mitigates these physical constraints by making its orb web from up to five different types of silks, closely controlling silk use and properties during web building. In particular, control of web geometry, silk tension, and silk stiffness allows spiders to adjust how vibrations spread throughout the web, as well as their amplitude and speed of propagation, which directly influences energy loss, distortion, and filtering. Turning to how spiders use this information, spiders use lyriform organs distributed across their eight legs as vibration sensors. Spiders can adjust coupling to the silk fibers and use posture to modify vibrational information as it moves from the web to the sensors. Spiders do not sense all vibrations equally—they are least sensitive to low frequencies (<30 Hz) and most sensitive to high frequencies (ca. 1 kHz). This sensitivity pattern cannot be explained purely by the frequency range of biological inputs. The role of physical and evolutionary constraints is discussed to explain spider vibration sensitivity and a role of vibration sensors to detect objects on the web as a form of echolocation is also discussed.
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Affiliation(s)
- B Mortimer
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
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61
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Scharff N, Coddington JA, Blackledge TA, Agnarsson I, Framenau VW, Szűts T, Hayashi CY, Dimitrov D. Phylogeny of the orb‐weaving spider family Araneidae (Araneae: Araneoidea). Cladistics 2019; 36:1-21. [DOI: 10.1111/cla.12382] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2019] [Indexed: 11/29/2022] Open
Affiliation(s)
- Nikolaj Scharff
- Center for Macroecology, Evolution and Climate Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- Smithsonian Institution National Museum of Natural History 10th and Constitution NW Washington DC 20560‐0105 USA
| | - Jonathan A. Coddington
- Smithsonian Institution National Museum of Natural History 10th and Constitution NW Washington DC 20560‐0105 USA
| | - Todd A. Blackledge
- Integrated Bioscience Program Department of Biology University of Akron Akron OH USA
| | - Ingi Agnarsson
- Smithsonian Institution National Museum of Natural History 10th and Constitution NW Washington DC 20560‐0105 USA
- Department of Biology University of Vermont 109 Carrigan Drive Burlington VT 05405‐0086 USA
| | - Volker W. Framenau
- Department of Terrestrial Zoology Western Australian Museum Locked Bag 49 Welshpool DC WA 6986 Australia
- School of Animal Biology University of Western Australia Crawley WA 6009 Australia
- Harry Butler Institute Murdoch University 90 South St. Murdoch WA 6150 Australia
| | - Tamás Szűts
- Center for Macroecology, Evolution and Climate Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- Department of Ecology University of Veterinary Medicine Budapest H1077 Budapest Hungary
| | - Cheryl Y. Hayashi
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics American Museum of Natural History New York NY 10024 USA
| | - Dimitar Dimitrov
- Center for Macroecology, Evolution and Climate Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- Natural History Museum University of Oslo PO Box 1172, Blindern NO‐0318 Oslo Norway
- Department of Natural History University Museum of Bergen University of Bergen Bergen Norway
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62
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Coddington JA, Agnarsson I, Hamilton CA, Bond JE. Spiders did not repeatedly gain, but repeatedly lost, foraging webs. PeerJ 2019; 7:e6703. [PMID: 30976470 PMCID: PMC6451839 DOI: 10.7717/peerj.6703] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/21/2019] [Indexed: 11/20/2022] Open
Abstract
Much genomic-scale, especially transcriptomic, data on spider phylogeny has accumulated in the last few years. These data have recently been used to investigate the diverse architectures and the origin of spider webs, concluding that the ancestral spider spun no foraging web, that spider webs evolved de novo 10-14 times, and that the orb web evolved at least three times. These findings in fact result from a particular phylogenetic character coding strategy, specifically coding the absence of webs as logically equivalent, and homologous to, 10 other observable (i.e., not absent) web architectures. "Absence" of webs should be regarded as inapplicable data. To be analyzed properly by character optimization algorithms, it should be coded as "?" because these codes-or their equivalent-are handled differently by such algorithms. Additional problems include critical misspellings of taxon names from one analysis to the next (misspellings cause some optimization algorithms to drop terminals, which affects taxon sampling and results), and mistakes in spider natural history. In sum, the method causes character optimization algorithms to produce counter-intuitive results, and does not distinguish absence from secondary loss. Proper treatment of missing entries and corrected data instead imply that foraging webs are primitive for spiders and that webs have been lost ∼5-7 times, not gained 10-14 times. The orb web, specifically, may be homologous (originated only once) although lost 2-6 times.
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Affiliation(s)
- Jonathan A. Coddington
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., USA
| | - Ingi Agnarsson
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., USA
- Department of Biology, University of Vermont, Burlington, VT, United States of America
| | - Chris A. Hamilton
- Department of Entomology, Plant Pathology, & Nematology, University of Idaho, Moscow, ID, United States of America
| | - Jason E. Bond
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, United States of America
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63
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Shin S, Clarke DJ, Lemmon AR, Moriarty Lemmon E, Aitken AL, Haddad S, Farrell BD, Marvaldi AE, Oberprieler RG, McKenna DD. Phylogenomic Data Yield New and Robust Insights into the Phylogeny and Evolution of Weevils. Mol Biol Evol 2019; 35:823-836. [PMID: 29294021 DOI: 10.1093/molbev/msx324] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The phylogeny and evolution of weevils (the beetle superfamily Curculionoidea) has been extensively studied, but many relationships, especially in the large family Curculionidae (true weevils; > 50,000 species), remain uncertain. We used phylogenomic methods to obtain DNA sequences from 522 protein-coding genes for representatives of all families of weevils and all subfamilies of Curculionidae. Most of our phylogenomic results had strong statistical support, and the inferred relationships were generally congruent with those reported in previous studies, but with some interesting exceptions. Notably, the backbone relationships of the weevil phylogeny were consistently strongly supported, and the former Nemonychidae (pine flower snout beetles) were polyphyletic, with the subfamily Cimberidinae (here elevated to Cimberididae) placed as sister group of all other weevils. The clade comprising the sister families Brentidae (straight-snouted weevils) and Curculionidae was maximally supported and the composition of both families was firmly established. The contributions of substitution modeling, codon usage and/or mutational bias to differences between trees reconstructed from amino acid and nucleotide sequences were explored. A reconstructed timetree for weevils is consistent with a Mesozoic radiation of gymnosperm-associated taxa to form most extant families and diversification of Curculionidae alongside flowering plants-first monocots, then other groups-beginning in the Cretaceous.
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Affiliation(s)
- Seunggwan Shin
- Department of Biological Sciences, University of Memphis, Memphis, TN
| | - Dave J Clarke
- Department of Biological Sciences, University of Memphis, Memphis, TN
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL
| | | | | | - Stephanie Haddad
- Department of Biological Sciences, University of Memphis, Memphis, TN
| | - Brian D Farrell
- Museum of Comparative Zoology, Harvard University, Cambridge, MA
| | - Adriana E Marvaldi
- CONICET, División Entomología, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | | | - Duane D McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN
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64
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Jiang CQ, Wang GY, Xiong J, Yang WT, Sun ZY, Feng JM, Warren A, Miao W. Insights into the origin and evolution of Peritrichia (Oligohymenophorea, Ciliophora) based on analyses of morphology and phylogenomics. Mol Phylogenet Evol 2019; 132:25-35. [DOI: 10.1016/j.ympev.2018.11.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 10/29/2018] [Accepted: 11/24/2018] [Indexed: 11/30/2022]
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65
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Narayanan Kutty S, Meusemann K, Bayless KM, Marinho MAT, Pont AC, Zhou X, Misof B, Wiegmann BM, Yeates D, Cerretti P, Meier R, Pape T. Phylogenomic analysis of Calyptratae: resolving the phylogenetic relationships within a major radiation of Diptera. Cladistics 2019; 35:605-622. [DOI: 10.1111/cla.12375] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2019] [Indexed: 12/21/2022] Open
Affiliation(s)
- Sujatha Narayanan Kutty
- Department of Biological Sciences National University of Singapore 14 Science Dr 4 Singapore 117543 Singapore
| | - Karen Meusemann
- Biology I, Evolutionary Biology & Ecology University of Freiburg Hauptstraße 1 Freiburg (Brsg.) Germany
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB) Bonn Germany
- Australian National Insect Collection CSIRO National Research Collections Australia (NRCA) Acton, ACT Canberra Australia
| | - Keith M. Bayless
- Department of Entomology California Academy of Sciences San Francisco CA USA
- Department of Entomology North Carolina State University Raleigh NC 27695 USA
| | - Marco A. T. Marinho
- Departamento de Ecologia, Zoologia e Genética Instituto de Biologia Universidade Federal de Pelotas Pelotas RS Brazil
| | - Adrian C. Pont
- Oxford University Museum of Natural History Parks Road Oxford OX1 3PW UK
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health China Agricultural University Beijing 100193 China
- Department of Entomology China Agricultural University Beijing 100193 China
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB) Bonn Germany
| | - Brian M. Wiegmann
- Department of Entomology North Carolina State University Raleigh NC 27695 USA
| | - David Yeates
- Australian National Insect Collection CSIRO National Research Collections Australia (NRCA) Acton, ACT Canberra Australia
| | - Pierfilippo Cerretti
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’ Sapienza Università di Roma Rome Italy
| | - Rudolf Meier
- Department of Biological Sciences National University of Singapore 14 Science Dr 4 Singapore 117543 Singapore
| | - Thomas Pape
- Natural History Museum of Denmark University of Copenhagen Universitetsparken 15 Copenhagen DK–2100 Denmark
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66
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Arthropod venoms: Biochemistry, ecology and evolution. Toxicon 2018; 158:84-103. [PMID: 30529476 DOI: 10.1016/j.toxicon.2018.11.433] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/20/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022]
Abstract
Comprising of over a million described species of highly diverse invertebrates, Arthropoda is amongst the most successful animal lineages to have colonized aerial, terrestrial, and aquatic domains. Venom, one of the many fascinating traits to have evolved in various members of this phylum, has underpinned their adaptation to diverse habitats. Over millions of years of evolution, arthropods have evolved ingenious ways of delivering venom in their targets for self-defence and predation. The morphological diversity of venom delivery apparatus in arthropods is astounding, and includes extensively modified pedipalps, tail (telson), mouth parts (hypostome), fangs, appendages (maxillulae), proboscis, ovipositor (stinger), and hair (urticating bristles). Recent investigations have also unravelled an astonishing venom biocomplexity with molecular scaffolds being recruited from a multitude of protein families. Venoms are a remarkable bioresource for discovering lead compounds in targeted therapeutics. Several components with prospective applications in the development of advanced lifesaving drugs and environment friendly bio-insecticides have been discovered from arthropod venoms. Despite these fascinating features, the composition, bioactivity, and molecular evolution of venom in several arthropod lineages remains largely understudied. This review highlights the prevalence of venom, its mode of toxic action, and the evolutionary dynamics of venom in Arthropoda, the most speciose phylum in the animal kingdom.
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67
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Wood HM, González VL, Lloyd M, Coddington J, Scharff N. Next-generation museum genomics: Phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea). Mol Phylogenet Evol 2018; 127:907-918. [DOI: 10.1016/j.ympev.2018.06.038] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/14/2018] [Accepted: 06/22/2018] [Indexed: 10/28/2022]
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68
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Ortiz D, Francke OF, Bond JE. A tangle of forms and phylogeny: Extensive morphological homoplasy and molecular clock heterogeneity in Bonnetina and related tarantulas. Mol Phylogenet Evol 2018; 127:55-73. [DOI: 10.1016/j.ympev.2018.05.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/25/2018] [Accepted: 05/13/2018] [Indexed: 12/13/2022]
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69
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Shao L, Li S. Early Cretaceous greenhouse pumped higher taxa diversification in spiders. Mol Phylogenet Evol 2018; 127:146-155. [PMID: 29803949 DOI: 10.1016/j.ympev.2018.05.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 05/14/2018] [Accepted: 05/19/2018] [Indexed: 12/13/2022]
Abstract
The Cretaceous experienced one of the most remarkable greenhouse periods in geological history. During this time, ecosystem reorganization significantly impacted the diversification of many groups of organisms. The rise of angiosperms marked a major biome turnover. Notwithstanding, relatively little remains known about how the Cretaceous global ecosystem impacted the evolution of spiders, which constitute one of the most abundant groups of predators. Herein, we evaluate the transcriptomes of 91 taxa representing more than half of the spider families. We add 23 newly sequenced taxa to the existing database to obtain a robust phylogenomic assessment. Phylogenetic reconstructions using different datasets and methods obtain novel placements of some groups, especially in the Synspermiata and the group having a retrolateral tibial apophysis (RTA). Molecular analyses indicate an expansion of the RTA clade at the Early Cretaceous with a hunting predatory strategy shift. Fossil analyses show a 7-fold increase of diversification rate at the same period, but this likely owes to the first occurrence of spiders in amber deposit. Additional analyses of fossil abundance show an accumulation of spider lineages in the Early Cretaceous. We speculate that the establishment of a warm greenhouse climate pumped the diversification of spiders, in particular among webless forms tracking the abundance of insect prey. Our study offers a new pathway for future investigations of spider phylogeny and diversification.
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Affiliation(s)
- Lili Shao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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70
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Lacava M, Camargo A, Garcia LF, Benamú MA, Santana M, Fang J, Wang X, Blamires SJ. Web building and silk properties functionally covary among species of wolf spider. J Evol Biol 2018; 31:968-978. [DOI: 10.1111/jeb.13278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/18/2018] [Accepted: 04/04/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Mariángeles Lacava
- Centro Universitario de Rivera Universidad de la República Rivera Uruguay
- Centro Universitario Regional del Este (CURE) Universidad de la República Treinta y Tres Uruguay
| | - Arley Camargo
- Centro Universitario de Rivera Universidad de la República Rivera Uruguay
| | - Luis F. Garcia
- Centro Universitario Regional del Este (CURE) Universidad de la República Treinta y Tres Uruguay
- Laboratorio Ecología del Comportamiento (IIBCE) Montevideo Uruguay
| | - Marco A. Benamú
- Centro Universitario de Rivera Universidad de la República Rivera Uruguay
- Laboratorio Ecología del Comportamiento (IIBCE) Montevideo Uruguay
| | - Martin Santana
- Laboratorio Ecología del Comportamiento (IIBCE) Montevideo Uruguay
| | - Jian Fang
- Institute for Frontier Materials (IFM) Deakin University Geelong Vic. Australia
| | - Xungai Wang
- Institute for Frontier Materials (IFM) Deakin University Geelong Vic. Australia
| | - Sean J. Blamires
- Evolution & Ecology Research Centre School of Biological, Earth & Environmental Sciences The University of New South Wales Sydney NSW Australia
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71
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Fernández R, Kallal RJ, Dimitrov D, Ballesteros JA, Arnedo MA, Giribet G, Hormiga G. Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life. Curr Biol 2018; 28:1489-1497.e5. [PMID: 29706520 DOI: 10.1016/j.cub.2018.03.064] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Accepted: 03/27/2018] [Indexed: 12/22/2022]
Abstract
Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators [1]. However, despite considerable effort [1-9], their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage diversification analyses. Our analyses, based on ca. 2,500 genes from 159 spider species, reject a single origin of the orb web (the "ancient orb-web hypothesis") and suggest that orb webs evolved multiple times since the late Triassic-Jurassic. We find no significant association between the loss of foraging webs and increases in diversification rates, suggesting that other factors (e.g., habitat heterogeneity or biotic interactions) potentially played a key role in spider diversification. Finally, we report notable genomic differences in the main spider lineages: while araneoids (ecribellate orb-weavers and their allies) reveal an enrichment in genes related to behavior and sensory reception, the retrolateral tibial apophysis (RTA) clade-the most diverse araneomorph spider lineage-shows enrichment in genes related to immune responses and polyphenic determination. This study, one of the largest invertebrate phylogenomic analyses to date, highlights the usefulness of transcriptomic data not only to build a robust backbone for the Spider Tree of Life, but also to address the genetic basis of diversification in the spider evolutionary chronicle.
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Affiliation(s)
- Rosa Fernández
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Robert J Kallal
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA
| | - Dimitar Dimitrov
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jesús A Ballesteros
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA
| | - Miquel A Arnedo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Department of Evolutionary Biology, Ecology and Environmental Sciences, & Biodiversity Research Institute (IRBio) Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA
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72
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Godwin RL, Opatova V, Garrison NL, Hamilton CA, Bond JE. Phylogeny of a cosmopolitan family of morphologically conserved trapdoor spiders (Mygalomorphae, Ctenizidae) using Anchored Hybrid Enrichment, with a description of the family, Halonoproctidae Pocock 1901. Mol Phylogenet Evol 2018; 126:303-313. [PMID: 29656103 DOI: 10.1016/j.ympev.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/08/2018] [Accepted: 04/06/2018] [Indexed: 02/08/2023]
Abstract
The mygalomorph family Ctenizidae has a world-wide distribution and currently contains nine genera and 135 species. However, the monophyly of this group has long been questioned on both morphological and molecular grounds. Here, we use Anchored Hybrid Enrichment (AHE) to gather hundreds of loci from across the genome for reconstructing the phylogenetic relationships among the nine genera and test the monophyly of the family. We also reconstruct the possible ancestral ranges of the most inclusive clade recovered. Using AHE, we generate a supermatrix of 565 loci and 115,209 bp for 27 individuals. For the first time, analyses using all nine genera produce results definitively establishing the non-monophyly of Ctenizidae. A lineage formed exclusively by representatives of South African Stasimopus was placed as the sister group to the remaining taxa in the tree, and the Mediterranean Cteniza and Cyrtocarenum were recovered with high support as sister to exemplars of Euctenizidae, Migidae, and Idiopidae. All the remaining genera-Bothriocyrtum, Conothele, Cyclocosmia, Hebestatis, Latouchia, and Ummidia-share a common ancestor. Based on these results, we formally elevate this clade to the level of family. Our results definitively establish both the non-monophyly of the Ctenizidae and non-validity of the subfamilies Ummidiinae and Ctenizinae. In order to establish the placement of the remaining three ctenizid genera, Cteniza, Cyrtocarenum, and Stasimopus, thorough analyses within the context of a complete mygalomorph phylogenetic framework are needed. We formally describe the family Halonoproctidae Pocock 1901 and infer that the family's most recent common ancestor was likely distributed in western North America and Asia.
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Affiliation(s)
- Rebecca L Godwin
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA.
| | - Vera Opatova
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA.
| | - Nicole L Garrison
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA.
| | - Chris A Hamilton
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | - Jason E Bond
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA.
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73
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Cheng DQ, Piel WH. The origins of the Psechridae: Web-building lycosoid spiders. Mol Phylogenet Evol 2018; 125:213-219. [PMID: 29635024 DOI: 10.1016/j.ympev.2018.03.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/21/2018] [Accepted: 03/30/2018] [Indexed: 01/09/2023]
Abstract
Psechrids are an enigmatic family of S.E. Asian spiders. This small family builds sheet webs and even orb webs, yet unlike other orb weavers, its putative relatives are largely cursorial lycosoids - a superfamily of approximately seven spider families related to wolf spiders. The orb web was invented at least twice: first in a very ancient event, and then second, within this clade of wolf-like spiders that reinvented this ability. Exactly how the spiders modified their silks, anatomy, and behaviors to accomplish this transition requires that we identify their precise evolutionary origins - yet, thus far, molecular phylogenies show poor support and considerable disagreement. Using phylogenomic methods based on whole body transcriptomes for psechrids and their putative relatives, we have recovered a well-supported phylogeny that places the Psechridae sister to the Ctenidae - a family of mostly cursorial habits but that, as with all psechrids, retains some cribellate species. Although this position reinforces the prevailing view that orb weaving in psechrids is largely a consequence of convergence, it is still possible that some components of this behavior are retained or resurrected in common with more distant true orb weaving ancestors.
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Affiliation(s)
- Dong-Qiang Cheng
- Yale-NUS College, 10 College Avenue West #01-101, Singapore 138609, Singapore
| | - William H Piel
- Yale-NUS College, 10 College Avenue West #01-101, Singapore 138609, Singapore; National University of Singapore, Department of Biological Sciences, Singapore.
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74
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Kallal RJ, Fernández R, Giribet G, Hormiga G. A phylotranscriptomic backbone of the orb-weaving spider family Araneidae (Arachnida, Araneae) supported by multiple methodological approaches. Mol Phylogenet Evol 2018; 126:129-140. [PMID: 29635025 DOI: 10.1016/j.ympev.2018.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/05/2018] [Accepted: 04/06/2018] [Indexed: 01/01/2023]
Abstract
The orb-weaving spider family Araneidae is extremely diverse (>3100 spp.) and its members can be charismatic terrestrial arthropods, many of them recognizable by their iconic orbicular snare web, such as the common garden spiders. Despite considerable effort to better understand their backbone relationships based on multiple sources of data (morphological, behavioral and molecular), pervasive low support remains in recent studies. In addition, no overarching phylogeny of araneids is available to date, hampering further comparative work. In this study, we analyze the transcriptomes of 33 taxa, including 19 araneids - 12 of them new to this study - representing most of the core family lineages, to examine the relationships within the family using genomic-scale datasets resulting from various methodological treatments, namely ortholog selection and gene occupancy as a measure of matrix completion. Six matrices were constructed to assess these effects by varying orthology inference method and gene occupancy threshold. Orthology methods used are the benchmarking tool BUSCO and the tree-based method UPhO; three gene occupancy thresholds (45%, 65%, 85%) were used to assess the effect of missing data. Gene tree and species tree-based methods (including multi-species coalescent and concatenation approaches, as well as maximum likelihood and Bayesian inference) were used totalling 17 analytical treatments. The monophyly of Araneidae and the placement of core araneid lineages were supported, together with some previously unsound backbone divergences; these include high support for Zygiellinae as the earliest diverging subfamily (followed by Nephilinae), the placement of Gasteracanthinae as sister group to Cyclosa and close relatives, and close relationships between the Araneus + Neoscona clade and Cyrtophorinae + Argiopinae clade. Incongruences were relegated to short branches in the clade comprising Cyclosa and its close relatives. We found congruence between most of the completed analyses, with minimal topological effects from occupancy/missing data and orthology assessment. The resulting number of genes by certain combinations of orthology and occupancy thresholds being analyzed had the greatest effect on the resulting trees, with anomalous outcomes recovered from analysis of lower numbers of genes.
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Affiliation(s)
- Robert J Kallal
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC 20052, USA.
| | - Rosa Fernández
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA; Bioinformatics and Genomics Unit, Center for Genomic Regulation, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC 20052, USA
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75
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Harvey MS, Hillyer MJ, Main BY, Moulds TA, Raven RJ, Rix MG, Vink CJ, Huey JA. Phylogenetic relationships of the Australasian open-holed trapdoor spiders (Araneae: Mygalomorphae: Nemesiidae: Anaminae): multi-locus molecular analyses resolve the generic classification of a highly diverse fauna. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx111] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Mark S Harvey
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag, Welshpool DC, Western Australia, Australia
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
- Adjunct, School of Natural Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West, New York, NY, USA
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA
| | - Mia J Hillyer
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag, Welshpool DC, Western Australia, Australia
| | - Barbara York Main
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Timothy A Moulds
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag, Welshpool DC, Western Australia, Australia
| | - Robert J Raven
- Biodiversity and Geosciences, Queensland Museum, South Brisbane, Queensland, Australia
| | - Michael G Rix
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag, Welshpool DC, Western Australia, Australia
- Biodiversity and Geosciences, Queensland Museum, South Brisbane, Queensland, Australia
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Cor J Vink
- Canterbury Museum, Rolleston Avenue, Christchurch, New Zeal
| | - Joel A Huey
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag, Welshpool DC, Western Australia, Australia
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
- Adjunct, School of Natural Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
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76
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Zhao Z, Li S. Extinction vs. Rapid Radiation: The Juxtaposed Evolutionary Histories of Coelotine Spiders Support the Eocene-Oligocene Orogenesis of the Tibetan Plateau. Syst Biol 2018; 66:988-1006. [PMID: 28431105 DOI: 10.1093/sysbio/syx042] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/24/2017] [Indexed: 11/14/2022] Open
Abstract
Evolutionary biology has long been concerned with how changing environments affect and drive the spatiotemporal development of organisms. Coelotine spiders (Agelenidae: Coelotinae) are common species in the temperate and subtropical areas of the Northern Hemisphere. Their long evolutionary history and the extremely imbalanced distribution of species richness suggest that Eurasian environments, especially since the Cenozoic, are the drivers of their diversification. We use phylogenetics, molecular dating, ancestral area reconstructions, diversity, and ecological niche analyses to investigate the spatiotemporal evolution of 286 coelotine species from throughout the region. Based on eight genes (6.5 kb) and 2323 de novo DNA sequences, analyses suggest an Eocene South China origin for them. Most extant, widespread species belong to the southern (SCG) or northern (NCG) clades. The origin of coelotine spiders appears to associate with either the Paleocene-Eocene Thermal Maximum or the hot period in early Eocene. Tibetan uplifting events influenced the current diversity patterns of coelotines. The origin of SCG lies outside of the Tibetan Plateau. Uplifting in the southeastern area of the plateau blocked dispersal since the Late Eocene. Continuous orogenesis appears to have created localized vicariant events, which drove rapid radiation in SCG. North-central Tibet is the likely location of origin for NCG and many lineages likely experienced extinction owing to uplifting since early Oligocene. Their evolutionary histories correspond with recent geological evidence that high-elevation orographical features existed in the Tibetan region as early as 40-35 Ma. Our discoveries may be the first empirical evidence that links the evolution of organisms to the Eocene-Oligocene uplifting of the Tibetan Plateau. [Tibet; biogeography; ecology; molecular clock; diversification.].
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Affiliation(s)
- Zhe Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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77
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Blom MPK, Bragg JG, Potter S, Moritz C. Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards. Syst Biol 2018; 66:352-366. [PMID: 28039387 DOI: 10.1093/sysbio/syw089] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 09/27/2016] [Indexed: 11/12/2022] Open
Abstract
Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ${\sim}2000$ exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well-supported topology based on all loci and find that a relatively small number of high-resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent-based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low-resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated in the analysis of empirical phylogenomic data sets. This will ultimately increase our confidence in species tree estimation using summary-coalescent methods and enable us to exploit genomic data for phylogenetic inference. [Coalescence; concatenation; Cryptoblepharus; exon capture; gene tree; phylogenomics; species tree.].
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Affiliation(s)
- Mozes P K Blom
- Research School of Biology, Australian National University, Canberra ACT 0200, Australia
| | - Jason G Bragg
- Research School of Biology, Australian National University, Canberra ACT 0200, Australia
| | - Sally Potter
- Research School of Biology, Australian National University, Canberra ACT 0200, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, Canberra ACT 0200, Australia
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78
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Alfaro RE, Griswold CE, Miller KB. -Comparative spigot ontogeny across the spider tree of life. PeerJ 2018; 6:e4233. [PMID: 29362692 PMCID: PMC5772386 DOI: 10.7717/peerj.4233] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022] Open
Abstract
Spiders are well known for their silk and its varying use across taxa. Very few studies have examined the silk spigot ontogeny of the entire spinning field of a spider. Historically the spider phylogeny was based on morphological data and behavioral data associated with silk. Recent phylogenomics studies have shifted major paradigms in our understanding of silk use evolution, reordering phylogenetic relationships that were once thought to be monophyletic. Considering this, we explored spigot ontogeny in 22 species, including Dolomedes tenebrosus and Hogna carolinensis, reported here for the first time. This is the first study of its kind and the first to incorporate the Araneae Tree of Life. After rigorous testing for phylogenetic signal and model fit, we performed 60 phylogenetic generalized least squares analyses on adult female and second instar spigot morphology. Six analyses had significant correlation coefficients, suggesting that instar, strategy, and spigot variety are good predictors of spigot number in spiders, after correcting for bias of shared evolutionary history. We performed ancestral character estimation of singular, fiber producing spigots on the posterior lateral spinneret whose potential homology has long been debated. We found that the ancestral root of our phylogram of 22 species, with the addition of five additional cribellate and ecribellate lineages, was more likely to have either none or a modified spigot rather than a pseudoflagelliform gland spigot or a flagelliform spigot. This spigot ontogeny approach is novel and we can build on our efforts from this study by growing the dataset to include deeper taxon sampling and working towards the capability to incorporate full ontogeny in the analysis.
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Affiliation(s)
- Rachael E. Alfaro
- Museum of Southwestern Biology, Division of Arthropods, University of New Mexico, Albuquerque, NM, United States of America
| | - Charles E. Griswold
- Entomology, California Academy of Sciences, San Francisco, CA, United States of America
| | - Kelly B. Miller
- Museum of Southwestern Biology, Division of Arthropods, University of New Mexico, Albuquerque, NM, United States of America
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79
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Chaw RC, Collin M, Wimmer M, Helmrick KL, Hayashi CY. Egg Case Silk Gene Sequences from Argiope Spiders: Evidence for Multiple Loci and a Loss of Function Between Paralogs. G3 (BETHESDA, MD.) 2018; 8:231-238. [PMID: 29127108 PMCID: PMC5765351 DOI: 10.1534/g3.117.300283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/08/2017] [Indexed: 12/22/2022]
Abstract
Spiders swath their eggs with silk to protect developing embryos and hatchlings. Egg case silks, like other fibrous spider silks, are primarily composed of proteins called spidroins (spidroin = spider-fibroin). Silks, and thus spidroins, are important throughout the lives of spiders, yet the evolution of spidroin genes has been relatively understudied. Spidroin genes are notoriously difficult to sequence because they are typically very long (≥ 10 kb of coding sequence) and highly repetitive. Here, we investigate the evolution of spider silk genes through long-read sequencing of Bacterial Artificial Chromosome (BAC) clones. We demonstrate that the silver garden spider Argiope argentata has multiple egg case spidroin loci with a loss of function at one locus. We also use degenerate PCR primers to search the genomic DNA of congeneric species and find evidence for multiple egg case spidroin loci in other Argiope spiders. Comparative analyses show that these multiple loci are more similar at the nucleotide level within a species than between species. This pattern is consistent with concerted evolution homogenizing gene copies within a genome. More complicated explanations include convergent evolution or recent independent gene duplications within each species.
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Affiliation(s)
- R Crystal Chaw
- Department of Biology, University of California, Riverside, California 92521
| | - Matthew Collin
- Department of Biology, University of California, Riverside, California 92521
| | - Marjorie Wimmer
- Department of Biology, University of California, Riverside, California 92521
| | - Kara-Leigh Helmrick
- Department of Biology, University of California, Riverside, California 92521
| | - Cheryl Y Hayashi
- Department of Biology, University of California, Riverside, California 92521
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024
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80
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Azevedo GHF, Griswold CE, Santos AJ. Systematics and evolution of ground spiders revisited (Araneae, Dionycha, Gnaphosidae). Cladistics 2017; 34:579-626. [DOI: 10.1111/cla.12226] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2017] [Indexed: 12/31/2022] Open
Affiliation(s)
- Guilherme H. F. Azevedo
- Departamento de Zoologia; Instituto de Ciências Biológicas; Universidade Federal de Minas Gerais. Av. Antônio, Carlos; 6627, 31270-901 Belo Horizonte MG Brazil
- Pós-graduação em Zoologia; Universidade Federal de Minas Gerais; Belo Horizonte MG Brazil
| | - Charles E. Griswold
- California Academy of Sciences; 55 Music Concourse Drive San Francisco CA 94118 USA
| | - Adalberto J. Santos
- Departamento de Zoologia; Instituto de Ciências Biológicas; Universidade Federal de Minas Gerais. Av. Antônio, Carlos; 6627, 31270-901 Belo Horizonte MG Brazil
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81
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Townley MA, Harms D. Comparative study of spinning field development in two species of araneophagic spiders (Araneae, Mimetidae, Australomimetus). EVOLUTIONARY SYSTEMATICS 2017. [DOI: 10.3897/evolsyst.1.14765] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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82
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Lüddecke T, Krehenwinkel H, Canning G, Glaw F, Longhorn SJ, Tänzler R, Wendt I, Vences M. Discovering the silk road: Nuclear and mitochondrial sequence data resolve the phylogenetic relationships among theraphosid spider subfamilies. Mol Phylogenet Evol 2017; 119:63-70. [PMID: 29104141 DOI: 10.1016/j.ympev.2017.10.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/14/2017] [Accepted: 10/22/2017] [Indexed: 02/06/2023]
Abstract
The mygalomorph spiders in the family Theraphosidae, also known as "tarantulas", are one of the most popular and diverse groups of arachnids, but their evolutionary history remains poorly understood because morphological analyses have only provided mostly controversial results, and a broad molecular perspective has been lacking until now. In this study we provide a preliminary molecular phylogenetic hypothesis of relationships among theraphosid subfamilies, based on 3.5 kbp of three nuclear and three mitochondrial markers, for 52 taxa representing 10 of the 11 commonly accepted subfamilies. Our analysis confirms the monophyly of the Theraphosidae and of most recognized theraphosid subfamilies, supports the validity of the Stromatopelminae and Poecilotheriinae, and indicates paraphyly of the Schismatothelinae. The placement of representatives of Schismatothelinae also indicates possible non-monophyly of Aviculariinae and supports the distinction of the previously contentious subfamily Psalmopoeinae. Major clades typically corresponded to taxa occurring in the same biogeographic region, with two of them each occurring in Africa, South America and Asia. Because relationships among these major clades were poorly supported, more extensive molecular data sets are required to test the hypothesis of independent colonization and multiple dispersal events among these continents.
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Affiliation(s)
- Tim Lüddecke
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany.
| | - Henrik Krehenwinkel
- Department of Environmental Science, Policy and Management, University of California Berkeley, 130 Mulford Hall #3114, Berkeley, CA 94720-3114, USA
| | - Gregory Canning
- Department of Nature Conservation, Tshwane University of Technology, P. Bag X680, Pretoria 0001, South Africa
| | - Frank Glaw
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247 München, Germany
| | - Stuart J Longhorn
- Hope Entomological Collections, Oxford University Museum of Natural History (OUMNH), Parks Road, Oxford, England OX1 3PW, United Kingdom
| | - René Tänzler
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247 München, Germany
| | - Ingo Wendt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
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83
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Sexual Dimorphism in the Lampshade Spider Hypochilus thorelli (Araneae: Hypochilidae). SOUTHEAST NAT 2017. [DOI: 10.1656/058.016.0315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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84
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Malay AD, Arakawa K, Numata K. Analysis of repetitive amino acid motifs reveals the essential features of spider dragline silk proteins. PLoS One 2017; 12:e0183397. [PMID: 28832627 PMCID: PMC5568437 DOI: 10.1371/journal.pone.0183397] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/03/2017] [Indexed: 12/19/2022] Open
Abstract
The extraordinary mechanical properties of spider dragline silk are dependent on the highly repetitive sequences of the component proteins, major ampullate spidroin 1 and 2 (MaSp2 and MaSp2). MaSp sequences are dominated by repetitive modules composed of short amino acid motifs; however, the patterns of motif conservation through evolution and their relevance to silk characteristics are not well understood. We performed a systematic analysis of MaSp sequences encompassing infraorder Araneomorphae based on the conservation of explicitly defined motifs, with the aim of elucidating the essential elements of MaSp1 and MaSp2. The results show that the GGY motif is nearly ubiquitous in the two types of MaSp, while MaSp2 is invariably associated with GP and di-glutamine (QQ) motifs. Further analysis revealed an extended MaSp2 consensus sequence in family Araneidae, with implications for the classification of the archetypal spidroins ADF3 and ADF4. Additionally, the analysis of RNA-seq data showed the expression of a set of distinct MaSp-like variants in genus Tetragnatha. Finally, an apparent association was uncovered between web architecture and the abundance of GP, QQ, and GGY motifs in MaSp2, which suggests a co-expansion of these motifs in response to the evolution of spiders' prey capture strategy.
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Affiliation(s)
- Ali D. Malay
- Enzyme Research Team, Center for Sustainable Resource Science, RIKEN, Wako-shi, Saitama, Japan
- * E-mail: (ADM); (KN)
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Kakuganji, Tsuruoka, Yamagata, Japan
| | - Keiji Numata
- Enzyme Research Team, Center for Sustainable Resource Science, RIKEN, Wako-shi, Saitama, Japan
- * E-mail: (ADM); (KN)
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85
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Evolutionary shifts in gene expression decoupled from gene duplication across functionally distinct spider silk glands. Sci Rep 2017; 7:8393. [PMID: 28827773 PMCID: PMC5566633 DOI: 10.1038/s41598-017-07388-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/28/2017] [Indexed: 11/08/2022] Open
Abstract
Spider silk synthesis is an emerging model for the evolution of tissue-specific gene expression and the role of gene duplication in functional novelty, but its potential has not been fully realized. Accordingly, we quantified transcript (mRNA) abundance in seven silk gland types and three non-silk gland tissues for three cobweb-weaving spider species. Evolutionary analyses based on expression levels of thousands of homologous transcripts and phylogenetic reconstruction of 605 gene families demonstrated conservation of expression for each gland type among species. Despite serial homology of all silk glands, the expression profiles of the glue-forming aggregate glands were divergent from fiber-forming glands. Also surprising was our finding that shifts in gene expression among silk gland types were not necessarily coupled with gene duplication, even though silk-specific genes belong to multi-paralog gene families. Our results challenge widely accepted models of tissue specialization and significantly advance efforts to replicate silk-based high-performance biomaterials.
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86
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Walter A, Bechsgaard J, Scavenius C, Dyrlund TS, Sanggaard KW, Enghild JJ, Bilde T. Characterisation of protein families in spider digestive fluids and their role in extra-oral digestion. BMC Genomics 2017; 18:600. [PMID: 28797246 PMCID: PMC5553785 DOI: 10.1186/s12864-017-3987-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/01/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Spiders are predaceous arthropods that are capable of subduing and consuming relatively large prey items compared to their own body size. For this purpose, spiders have evolved potent venoms to immobilise prey and digestive fluids that break down nutrients inside the prey's body by means of extra-oral digestion (EOD). Both secretions contain an array of active proteins, and an overlap of some components has been anecdotally reported, but not quantified. We systematically investigated the extent of such protein overlap. As venom injection and EOD succeed each other, we further infer functional explanations, and, by comparing two spider species belonging to different clades, assess its adaptive significance for spider EOD in general. RESULTS We describe the protein composition of the digestive fluids of the mygalomorph Acanthoscurria geniculata and the araneomorph Stegodyphus mimosarum, in comparison with previously published data on a third spider species. We found a number of similar hydrolases being highly abundant in all three species. Among them, members of the family of astacin-like metalloproteases were particularly abundant. While the importance of these proteases in spider venom and digestive fluid was previously noted, we now highlight their widespread use across different spider taxa. Finally, we found species specific differences in the protein overlap between venom and digestive fluid, with the difference being significantly greater in S. mimosarum compared to A. geniculata. CONCLUSIONS The injection of venom precedes the injection with digestive fluid, and the overlap of proteins between venom and digestive fluid suggests an early involvement in EOD. Species specific differences in the overlap may reflect differences in ecology between our two study species. The protein composition of the digestive fluid of all the three species we compared is highly similar, suggesting that the cocktail of enzymes is highly conserved and adapted to spider EOD.
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Affiliation(s)
- André Walter
- Department of Bioscience, Aarhus University, Aarhus, Denmark.
| | | | - Carsten Scavenius
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Thomas S Dyrlund
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kristian W Sanggaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Aarhus, Denmark
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87
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Turner SP, Longhorn SJ, Hamilton CA, Gabriel R, PÉrez-Miles F, Vogler AP. Re-evaluating conservation priorities of New World tarantulas (Araneae: Theraphosidae) in a molecular framework indicates non-monophyly of the genera, Aphonopelma and Brachypelma. SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1346719] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Steven P. Turner
- The Natural History Museum (NHM), Cromwell Road, South Kensington, London, UK
- Beneficial Insect Laboratory, North Carolina Department of Agriculture and Consumer Services, Cary, North Carolina, USA
| | | | - Chris A. Hamilton
- Auburn University Museum of Natural History (AUMNH), and Dept. Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Ray Gabriel
- Oxford Museum of Natural History (OUMNH), Parks Road, Oxford, UK
| | | | - Alfried P. Vogler
- The Natural History Museum (NHM), Cromwell Road, South Kensington, London, UK
- Imperial College London, South Kensington, London, UK
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88
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Harrison SE, Harvey MS, Cooper SJB, Austin AD, Rix MG. Across the Indian Ocean: A remarkable example of trans-oceanic dispersal in an austral mygalomorph spider. PLoS One 2017; 12:e0180139. [PMID: 28767648 PMCID: PMC5540276 DOI: 10.1371/journal.pone.0180139] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/09/2017] [Indexed: 11/17/2022] Open
Abstract
The Migidae are a family of austral trapdoor spiders known to show a highly restricted and disjunct distribution pattern. Here, we aim to investigate the phylogeny and historical biogeography of the group, which was previously thought to be vicariant in origin, and examine the biogeographic origins of the genus Moggridgea using a dated multi-gene phylogeny. Moggridgea specimens were sampled from southern Australia and Africa, and Bertmainus was sampled from Western Australia. Sanger sequencing methods were used to generate a robust six marker molecular dataset consisting of the nuclear genes 18S rRNA, 28S rRNA, ITS rRNA, XPNPEP3 and H3 and the mitochondrial gene COI. Bayesian and Maximum Likelihood methods were used to analyse the dataset, and the key dispersal nodes were dated using BEAST. Based on our data, we demonstrate that Moggridgea rainbowi from Kangaroo Island, Australia is a valid member of the otherwise African genus Moggridgea. Molecular clock dating analyses show that the inter-specific divergence of M. rainbowi from African congeners is between 2.27-16.02 million years ago (Mya). This divergence date significantly post-dates the separation of Africa from Gondwana (95 Mya) and therefore does not support a vicariant origin for Australian Moggridgea. It also pre-dates human colonisation of Kangaroo Island, a result which is further supported by the intra-specific divergence date of 1.10-6.39 Mya between separate populations on Kangaroo Island. These analyses provide strong support for the hypothesis that Moggridgea colonised Australia via long-distance trans-Indian Ocean dispersal, representing the first such documented case in a mygalomorph spider.
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Affiliation(s)
- Sophie E Harrison
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Mark S Harvey
- Department of Terrestrial Zoology, Western Australian Museum, Welshpool DC, WA, Australia.,School of Biology, The University of Western Australia, Crawley, WA, Australia.,School of Natural Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Steve J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.,Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Michael G Rix
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.,Department of Terrestrial Zoology, Western Australian Museum, Welshpool DC, WA, Australia.,Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, QLD, Australia
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89
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Morehouse NI, Buschbeck EK, Zurek DB, Steck M, Porter ML. Molecular Evolution of Spider Vision: New Opportunities, Familiar Players. THE BIOLOGICAL BULLETIN 2017; 233:21-38. [PMID: 29182503 DOI: 10.1086/693977] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Spiders are among the world's most species-rich animal lineages, and their visual systems are likewise highly diverse. These modular visual systems, composed of four pairs of image-forming "camera" eyes, have taken on a huge variety of forms, exhibiting variation in eye size, eye placement, image resolution, and field of view, as well as sensitivity to color, polarization, light levels, and motion cues. However, despite this conspicuous diversity, our understanding of the genetic underpinnings of these visual systems remains shallow. Here, we review the current literature, analyze publicly available transcriptomic data, and discuss hypotheses about the origins and development of spider eyes. Our efforts highlight that there are many new things to discover from spider eyes, and yet these opportunities are set against a backdrop of deep homology with other arthropod lineages. For example, many (but not all) of the genes that appear important for early eye development in spiders are familiar players known from the developmental networks of other model systems (e.g., Drosophila). Similarly, our analyses of opsins and related phototransduction genes suggest that spider photoreceptors employ many of the same genes and molecular mechanisms known from other arthropods, with a hypothesized ancestral spider set of four visual and four nonvisual opsins. This deep homology provides a number of useful footholds into new work on spider vision and the molecular basis of its extant variety. We therefore discuss what some of these first steps might be in the hopes of convincing others to join us in studying the vision of these fascinating creatures.
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Key Words
- AL, anterior lateral
- AM, anterior median
- BLAST, Basic Local Alignment Search Tool
- CNS, central nervous system
- KAAS, KEGG Automatic Annotation Server
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LWS, long wavelength sensitive
- MAFFT, Multiple Alignment using Fast Fourier Transform
- MWS, middle wavelength sensitive
- PL, posterior lateral
- PM, posterior median
- RAxML, Randomized Axelerated Maximum Likelihood
- UVS, ultraviolet sensitive
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90
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Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 2017. [PMID: 28756775 DOI: 10.1186/s12915-017-0399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. RESULTS We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. CONCLUSIONS Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.
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Affiliation(s)
- Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Thomas Clarke
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Torsten Wierschin
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
| | - Matthias Pechmann
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan
- Osaka Medical College, Takatsuki, Osaka, Japan
| | - Lauren Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Alexandra D Buffry
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cornelius Eibner
- Department of Genetics, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Peter Funch
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Luis B Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Vanessa L Gonzalez
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Sam Griffiths-Jones
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cheryl Hayashi
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rodrigo Nunes da Fonseca
- Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, 27941-222, Brazil
| | - Christian L B Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Matthew Ronshaugen
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christoph Schomburg
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Montserrat Torres-Oliva
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Natascha Turetzek
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
- Evolution and Optics of Nanostructure group (EON), Biology Department, Ghent University, Gent, Belgium
| | - John H Werren
- Biology Department, University of Rochester, Rochester, NY, 14627, USA
| | - Carsten Wolff
- Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115, Berlin, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077, Göttingen, Germany.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jonathan Coddington
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA.
| | - Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Mario Stanke
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.
| | - Nikola-Michael Prpic
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Nico Posnien
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 2017; 15:62. [PMID: 28756775 PMCID: PMC5535294 DOI: 10.1186/s12915-017-0399-x] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/21/2017] [Indexed: 12/15/2022] Open
Abstract
Background The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. Results We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Conclusions Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0399-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.,Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Thomas Clarke
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.,Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA.,J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Torsten Wierschin
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
| | - Matthias Pechmann
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.,Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.,Osaka Medical College, Takatsuki, Osaka, Japan
| | - Lauren Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Alexandra D Buffry
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cornelius Eibner
- Department of Genetics, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Peter Funch
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Luis B Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Vanessa L Gonzalez
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Sam Griffiths-Jones
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cheryl Hayashi
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.,Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rodrigo Nunes da Fonseca
- Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, 27941-222, Brazil
| | - Christian L B Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Matthew Ronshaugen
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christoph Schomburg
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Montserrat Torres-Oliva
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Natascha Turetzek
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark.,Evolution and Optics of Nanostructure group (EON), Biology Department, Ghent University, Gent, Belgium
| | - John H Werren
- Biology Department, University of Rochester, Rochester, NY, 14627, USA
| | - Carsten Wolff
- Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115, Berlin, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077, Göttingen, Germany.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jonathan Coddington
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA.
| | - Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan. .,Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Mario Stanke
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.
| | - Nikola-Michael Prpic
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Nico Posnien
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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92
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Piorkowski D, Blackledge TA. Punctuated evolution of viscid silk in spider orb webs supported by mechanical behavior of wet cribellate silk. Naturwissenschaften 2017; 104:67. [DOI: 10.1007/s00114-017-1489-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/01/2017] [Accepted: 07/04/2017] [Indexed: 01/09/2023]
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93
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Vink CJ. A history of araneology in New Zealand. J R Soc N Z 2017. [DOI: 10.1080/03036758.2017.1334676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Cor J. Vink
- Canterbury Museum, Christchurch, New Zealand
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94
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Ortiz D, Francke OF. Reconciling morphological and molecular systematics in tarantulas (Araneae: Theraphosidae): revision of the Mexican endemic genus Bonnetina. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlw013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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95
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The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression. Nat Genet 2017; 49:895-903. [PMID: 28459453 DOI: 10.1038/ng.3852] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/29/2017] [Indexed: 12/11/2022]
Abstract
Spider silks are the toughest known biological materials, yet are lightweight and virtually invisible to the human immune system, and they thus have revolutionary potential for medicine and industry. Spider silks are largely composed of spidroins, a unique family of structural proteins. To investigate spidroin genes systematically, we constructed the first genome of an orb-weaving spider: the golden orb-weaver (Nephila clavipes), which builds large webs using an extensive repertoire of silks with diverse physical properties. We cataloged 28 Nephila spidroins, representing all known orb-weaver spidroin types, and identified 394 repeated coding motif variants and higher-order repetitive cassette structures unique to specific spidroins. Characterization of spidroin expression in distinct silk gland types indicates that glands can express multiple spidroin types. We find evidence of an alternatively spliced spidroin, a spidroin expressed only in venom glands, evolutionary mechanisms for spidroin diversification, and non-spidroin genes with expression patterns that suggest roles in silk production.
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96
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Abstract
There is a tension between the conception of cognition as a central nervous system (CNS) process and a view of cognition as extending towards the body or the contiguous environment. The centralised conception requires large or complex nervous systems to cope with complex environments. Conversely, the extended conception involves the outsourcing of information processing to the body or environment, thus making fewer demands on the processing power of the CNS. The evolution of extended cognition should be particularly favoured among small, generalist predators such as spiders, and here, we review the literature to evaluate the fit of empirical data with these contrasting models of cognition. Spiders do not seem to be cognitively limited, displaying a large diversity of learning processes, from habituation to contextual learning, including a sense of numerosity. To tease apart the central from the extended cognition, we apply the mutual manipulability criterion, testing the existence of reciprocal causal links between the putative elements of the system. We conclude that the web threads and configurations are integral parts of the cognitive systems. The extension of cognition to the web helps to explain some puzzling features of spider behaviour and seems to promote evolvability within the group, enhancing innovation through cognitive connectivity to variable habitat features. Graded changes in relative brain size could also be explained by outsourcing information processing to environmental features. More generally, niche-constructed structures emerge as prime candidates for extending animal cognition, generating the selective pressures that help to shape the evolving cognitive system.
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Affiliation(s)
- Hilton F Japyassú
- Biology Institute, Federal University of Bahia, Rua Barão de Jeremoabo s/n, Campus de Ondina, Salvador, Bahia, 40170-115, Brazil.
- Centre for Biodiversity, School of Biology, University of St Andrews, Harold Mitchell Building, St Andrews, Fife, UK, KY16 9TH.
| | - Kevin N Laland
- Centre for Biodiversity, School of Biology, University of St Andrews, Harold Mitchell Building, St Andrews, Fife, UK, KY16 9TH
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97
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Vienneau-Hathaway JM, Brassfield ER, Lane AK, Collin MA, Correa-Garhwal SM, Clarke TH, Schwager EE, Garb JE, Hayashi CY, Ayoub NA. Duplication and concerted evolution of MiSp-encoding genes underlie the material properties of minor ampullate silks of cobweb weaving spiders. BMC Evol Biol 2017; 17:78. [PMID: 28288560 PMCID: PMC5348893 DOI: 10.1186/s12862-017-0927-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 02/24/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Orb-web weaving spiders and their relatives use multiple types of task-specific silks. The majority of spider silk studies have focused on the ultra-tough dragline silk synthesized in major ampullate glands, but other silk types have impressive material properties. For instance, minor ampullate silks of orb-web weaving spiders are as tough as draglines, due to their higher extensibility despite lower strength. Differences in material properties between silk types result from differences in their component proteins, particularly members of the spidroin (spider fibroin) gene family. However, the extent to which variation in material properties within a single silk type can be explained by variation in spidroin sequences is unknown. Here, we compare the minor ampullate spidroins (MiSp) of orb-weavers and cobweb weavers. Orb-web weavers use minor ampullate silk to form the auxiliary spiral of the orb-web while cobweb weavers use it to wrap prey, suggesting that selection pressures on minor ampullate spidroins (MiSp) may differ between the two groups. RESULTS We report complete or nearly complete MiSp sequences from five cobweb weaving spider species and measure material properties of minor ampullate silks in a subset of these species. We also compare MiSp sequences and silk properties of our cobweb weavers to published data for orb-web weavers. We demonstrate that all our cobweb weavers possess multiple MiSp loci and that one locus is more highly expressed in at least two species. We also find that the proportion of β-spiral-forming amino acid motifs in MiSp positively correlates with minor ampullate silk extensibility across orb-web and cobweb weavers. CONCLUSIONS MiSp sequences vary dramatically within and among spider species, and have likely been subject to multiple rounds of gene duplication and concerted evolution, which have contributed to the diverse material properties of minor ampullate silks. Our sequences also provide templates for recombinant silk proteins with tailored properties.
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Affiliation(s)
| | | | - Amanda Kelly Lane
- Department of Biology, Washington and Lee University, Lexington, VA USA
| | | | | | - Thomas H. Clarke
- Department of Biology, Washington and Lee University, Lexington, VA USA
- Department of Biology, University of California, Riverside, CA USA
| | - Evelyn E. Schwager
- Department of Biological Sciences, University of Massachusetts, Lowell, MA USA
| | - Jessica E. Garb
- Department of Biological Sciences, University of Massachusetts, Lowell, MA USA
| | | | - Nadia A. Ayoub
- Department of Biology, Washington and Lee University, Lexington, VA USA
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98
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Fernández R, Sharma PP, Tourinho AL, Giribet G. The Opiliones tree of life: shedding light on harvestmen relationships through transcriptomics. Proc Biol Sci 2017; 284:20162340. [PMID: 28228511 PMCID: PMC5326524 DOI: 10.1098/rspb.2016.2340] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/27/2017] [Indexed: 12/12/2022] Open
Abstract
Opiliones are iconic arachnids with a Palaeozoic origin and a diversity that reflects ancient biogeographic patterns dating back at least to the times of Pangea. Owing to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to infer their systematic relationships. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level. Here, we analysed a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing approximately 80% of the extant familial diversity in Opiliones. Our phylogenetic analyses, including a set of data matrices with different gene occupancy and evolutionary rates, and using a multitude of methods correcting for a diversity of factors affecting phylogenomic data matrices, provide a robust and stable Opiliones tree of life, where most families and higher taxa are precisely placed. Our dating analyses using alternative calibration points, methods and analytical parameters provide well-resolved old divergences, consistent with ancient regionalization in Pangea in some groups, and Pangean vicariance in others. The integration of state-of-the-art molecular techniques and analyses, together with the broadest taxonomic sampling to date presented in a phylogenomic study of harvestmen, provide new insights into harvestmen interrelationships, as well as an overview of the general biogeographic patterns of this ancient arthropod group.
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Affiliation(s)
- Rosa Fernández
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 352 Birge Hall, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Ana Lúcia Tourinho
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade (CBIO), Avenida André Araújo, 2936, Aleixo, CEP 69011-970, Manaus, Amazonas, Brazil
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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99
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Chaw RC, Saski CA, Hayashi CY. Complete gene sequence of spider attachment silk protein (PySp1) reveals novel linker regions and extreme repeat homogenization. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 81:80-90. [PMID: 28057598 DOI: 10.1016/j.ibmb.2017.01.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 12/27/2016] [Accepted: 01/01/2017] [Indexed: 06/06/2023]
Abstract
Spiders use a myriad of silk types for daily survival, and each silk type has a unique suite of task-specific mechanical properties. Of all spider silk types, pyriform silk is distinct because it is a combination of a dry protein fiber and wet glue. Pyriform silk fibers are coated with wet cement and extruded into "attachment discs" that adhere silks to each other and to substrates. The mechanical properties of spider silk types are linked to the primary and higher-level structures of spider silk proteins (spidroins). Spidroins are often enormous molecules (>250 kDa) and have a lengthy repetitive region that is flanked by relatively short (∼100 amino acids), non-repetitive amino- and carboxyl-terminal regions. The amino acid sequence motifs in the repetitive region vary greatly between spidroin type, while motif length and number underlie the remarkable mechanical properties of spider silk fibers. Existing knowledge of pyriform spidroins is fragmented, making it difficult to define links between the structure and function of pyriform spidroins. Here, we present the full-length sequence of the gene encoding pyriform spidroin 1 (PySp1) from the silver garden spider Argiope argentata. The predicted protein is similar to previously reported PySp1 sequences but the A. argentata PySp1 has a uniquely long and repetitive "linker", which bridges the amino-terminal and repetitive regions. Predictions of the hydrophobicity and secondary structure of A. argentata PySp1 identify regions important to protein self-assembly. Analysis of the full complement of A. argentata PySp1 repeats reveals extreme intragenic homogenization, and comparison of A. argentata PySp1 repeats with other PySp1 sequences identifies variability in two sub-repetitive expansion regions. Overall, the full-length A. argentata PySp1 sequence provides new evidence for understanding how pyriform spidroins contribute to the properties of pyriform silk fibers.
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Affiliation(s)
- Ro Crystal Chaw
- Department of Biology, University of California, Riverside, 900 University Ave., Riverside, 92521 CA, USA.
| | - Christopher A Saski
- Clemson University Genomics and Computational Biology Facility, Institute for Translational Genomics, Biosystems Research Complex #310, 105 Collings St., Clemson, 29634 SC, USA.
| | - Cheryl Y Hayashi
- Department of Biology, University of California, Riverside, 900 University Ave., Riverside, 92521 CA, USA; Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.
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100
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Blamires SJ, Blackledge TA, Tso IM. Physicochemical Property Variation in Spider Silk: Ecology, Evolution, and Synthetic Production. ANNUAL REVIEW OF ENTOMOLOGY 2017; 62:443-460. [PMID: 27959639 DOI: 10.1146/annurev-ento-031616-035615] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The unique combination of great stiffness, strength, and extensibility makes spider major ampullate (MA) silk desirable for various biomimetic and synthetic applications. Intensive research on the genetics, biochemistry, and biomechanics of this material has facilitated a thorough understanding of its properties at various levels. Nevertheless, methods such as cloning, recombination, and electrospinning have not successfully produced materials with properties as impressive as those of spider silk. It is nevertheless becoming clear that silk properties are a consequence of whole-organism interactions with the environment in addition to genetic expression, gland biochemistry, and spinning processes. Here we assimilate the research done and assess the techniques used to determine distinct forms of spider silk chemical and physical property variability. We suggest that more research should focus on testing hypotheses that explain spider silk property variations in ecological and evolutionary contexts.
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Affiliation(s)
- Sean J Blamires
- Department of Life Science, Tunghai University, Taichung 40704, Taiwan;
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental Sciences, The University of New South Wales, Sydney 2052, Australia;
| | - Todd A Blackledge
- Department of Biology, Integrated Bioscience Program, The University of Akron, Akron, Ohio 44325;
| | - I-Min Tso
- Department of Life Science, Tunghai University, Taichung 40704, Taiwan;
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