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A Molecular Approach to the Phylogeny of Theraphosidae and Their Kin

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New World Tarantulas

Part of the book series: Zoological Monographs ((ZM,volume 6))

Abstract

Molecular data are increasingly helping inform tarantula evolutionary history. This includes redefining taxonomic groups at many levels, from clarifying species limits and matching sexes to elucidating the boundaries of genera and higher taxonomic ranks. We initially overview early molecular studies with tarantulas, before more closely looking at later developments with either a focus on questions around the population–species interface, or on aspects of the broader phylogeny. In both, we consider the gene fragments used for insights, but also introduce the role that newer high-throughput sequencing can play to expand the scope of such datasets. We then move into other approaches offered by the age of genomics, with some focus on mitogenomics versus nuclear genomics. Here we discuss some useful aspects of genomes such as gene arrangements that may be treated as “rare-events” to resolve intractable systematic questions. We then overview transcriptomic methods versus target capture approaches, each of which provide increasingly powerful methods for new insights. Finally, we speculate on where additional taxon sampling is needed to resolve the tarantula phylogeny, before concluding how existing studies now form a solid baseline for future projects, in particular on biogeography or the evolution of body size, venom, or other interesting comparative questions.

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Notes

  1. 1.

    The name “Eurypelma californicum” was used in over 100 studies mainly of biochemistry, with the likely identity being Aphonopelma hentzi (Nentwig 2012).

References

  • Agnarsson I, Coddington J, Kuntner M (2013) Systematics – progress in the study of spider diversity and evolution. In: Penney D (ed) Spider research in the 21st century – trends and perspectives. Siri Scientific Press, Manchester, pp 58–111

    Google Scholar 

  • Alamo L, Pinto A, Sulbarán G, Mavárez J, Padrón R (2018) Lessons from a tarantula: new insights into myosin interacting-heads motif evolution and its implications on disease. Biophys Rev 10(5):1465–1477

    Article  CAS  PubMed  Google Scholar 

  • Altenhoff AM, Gil M, Gonnet GH, Dessimoz C (2013) Inferring hierarchical orthologous groups from orthologous gene pairs. PLoS One 8(1):e53786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Andre C, Hüsser M (2018) About trapdoors and bridges – new insights in the little-known ecology and lifestyle of the genus Typhochlaena C.L. Koch 1850. J Br Tarantula Soc 32(3):3–29

    Google Scholar 

  • Arnedo MA, Ferrández MA (2007) Mitochondrial markers reveal deep population subdivisión in the European protected spider Macrothele calpeiana (Walckenaer, 1805) (Araneae, Hexathelidae). Cons Genetics 8:1147–1162

    Article  CAS  Google Scholar 

  • Astrin JJ, Huber BA, Misof B, Klütsch CFC (2006) Molecular taxonomy in pholcid spiders (Pholcidae, Araneae): evaluation of species identification methods using CO1 and 16S rRNA. Zool Scr 35:441–457

    Article  Google Scholar 

  • Ayoub NA, Garb JE, Hedin M, Hayashi CY (2007) Utility of the nuclear protein-coding gene, elongation factor-1 gamma (EF-1y) for spider systematics, emphasizing family level relationships of tarantulas and their kin (Araneae: Mygalomorphae). Mol Phylogenet Evol 42(2):394–409

    Article  CAS  PubMed  Google Scholar 

  • Babb PL, Lahens NF, Correa-Garhwal SM, Nicholson DN, Kim EJ, Hogenesch JB, Kuntner M, Higgins L, Hayashi CY, Agnarsson I, Voight BF (2017) The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression. Nat Genet 49(6):895–903

    Article  CAS  PubMed  Google Scholar 

  • Bailey AL, Brewer MS, Hendrixson BE, Bond JE (2010) Phylogeny and classification of the trapdoor genus Myrmekiaphila: an integrative approach to evaluating taxonomic hypotheses. PLoS One 5:e12744

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ballard JWO, Olsen GJ, Faith DP, Odgers WA, Rowell DM, Atkinson PW (1992) Evidence from 12S ribosomal RNA sequences that Onychophorans are modified arthropods. Science 258:1345–1348

    Article  CAS  PubMed  Google Scholar 

  • Ballesteros JA, Hormiga G (2016) A new orthology assessment method for phylogenomic data: unrooted phylogenetic orthology. Mol Biol Evol 33:2117–2134

    Article  CAS  PubMed  Google Scholar 

  • Ballesteros JA, Sharma PP (2019) A critical appraisal of the placement of Xiphosura (Chelicerata) with account of known sources of phylogenetic error. Syst Biol 68(6):896–917

    Article  PubMed  CAS  Google Scholar 

  • Barrett RDH, Hebert PDN (2005) Identifying spiders through DNA barcodes. Can J Zool 83:481–491

    Article  CAS  Google Scholar 

  • Beavis AS, Sunnucks P, Roswell DM (2011) Microhabitat preferences drive phylogeographic disparities in two Australian funnel web spiders. Biol J Linn Soc 104:805–819

    Article  Google Scholar 

  • Blagoev GA, Nikolova NI, Sobel CN, Hebert PDN, Adamowicz SJ (2013) Spiders (Araneae) of Churchill, Manitoba: DNA barcodes and morphology reveal high species diversity and new Canadian records. BMC Ecol 13:e44

    Article  Google Scholar 

  • Blagoev GA, DeWaard JR, Ratnasingham S, DeWaard SL, Lu L, Robertson J, Telfer AC, Hebert PDN (2016) Untangling taxonomy: a DNA barcode reference library for Canadian spiders. Mol Ecol Resour 16:325–341

    Article  CAS  PubMed  Google Scholar 

  • Blaimer BB, Lloyd MW, Guillory WX, Brady SG (2016) Sequence capture and phylogenetic utility of genomic Ultraconserved Elements obtained from pinned insect specimens. PLoS One 11:e0161531–e0161520

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bond JE (2004) Systematics of the Californian euctenizine spider genus Apomastus (Araneae: Mygalomorphae: Cyrtauchenidae): the relationship between molecular and morphological taxonomy. Invertebr Syst 18:361–376

    Article  CAS  Google Scholar 

  • Bond JE (2012) Phylogenetic treatment and taxonomic revision of the trapdoor spider genus Apostichus Simon (Araneae, Mygalomorphae, Euctenizidae). ZooKeys 252:1–209

    Article  Google Scholar 

  • Bond JE, Hendrixson BE, Hamilton CA, Hedin M (2012) A reconsideration of the classification of the spider infraorder Mygalomorphae (Arachnida: Araneae) based on three nuclear genes and morphology. PLoS One 7:e38753

    Google Scholar 

  • Bond JE, Hedin MC (2006) A total evidence assessment of the phylogeny of North American euctenizine trapdoor spiders (Araneae, Mygalomorphae, Cyrtaucheniidae) using Bayesian inference. Mol Phylogenet Evol 41:70–85

    Article  CAS  PubMed  Google Scholar 

  • Bond JE, Stockman AK (2008) An integrative method for delimiting cohesion species: finding the population-species interface in a group of Californian trapdoor spiders with extreme genetic divergence and geographic structuring. Syst Biol 57:628–646

    Article  CAS  PubMed  Google Scholar 

  • Bond JE, Hedin MC, Ramirez MG, Opell BD (2001) Deep molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spider Aptostichus simus. Mol Ecol 10:899–910

    Article  CAS  PubMed  Google Scholar 

  • Bond JE, Beamer DA, Lamb T, Hedin M (2006) Combining genetic and geospatial analyses to infer population extinction in mygalomorph spiders endemic to the Los Angeles region. Anim Conserv 9:145–157

    Article  Google Scholar 

  • Bond JE, Garrison NL, Hamilton CA, Godwin RL, Hedin M, Agnarsson I (2014) Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution. Curr Biol 24:1765–1771

    Article  CAS  PubMed  Google Scholar 

  • Boore JL, Collins TM, Stanton D, Daehler LL, Brown WM (1995) Deducing the pattern of arthropod phylogeny from mitochondrial DNA re-arrangements. Nature 376:163–167

    Article  CAS  PubMed  Google Scholar 

  • Branstetter MG, Danforth BN, Pitts JP, Faircloth BC, Ward PS, Buffington ML, Gates MW, Kula RR, Brady SG (2017a) Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees. Curr Biol 27:1019–1025

    Article  CAS  PubMed  Google Scholar 

  • Branstetter MG, Longino JT, Ward PS, Faircloth BC (2017b) Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera. Methods Ecol Evol 8:768–776

    Article  Google Scholar 

  • Brewer MS, Cotoras DD, Croucher PJP, Gillespie RG (2014) New sequencing technologies, the development of genomics tools, and their applications in evolutionary arachnology. J Arachnol 42:1–15

    Article  Google Scholar 

  • Briscoe AG, Goodacre S, Masta SE, Taylor MI, Arnedo MA, Penny D, Kenny J, Creer S (2013) Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics? A case study within spiders (Arthropoda: Araneae). PLoS One 8:e62404

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, Udall JA, Wilcox ER, Crandall KA (2011) Targeted amplicon sequencing (TAS): a scalable next-gen approach to multi-locus, multi-taxa phylogenetics. Genome Biol Evol 3:1312–1323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cao Z, Yu Y, Wu Y, Hao P, Di Z, He Y, Chen Z, Yang W, Shen Z, He X et al (2013) The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods. Nat Commun 4:2602

    Article  PubMed  CAS  Google Scholar 

  • Carlson DE, Hedin M (2017) Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegyne), with emphasis on molecular evolution of orphan genes. PLoS One 12:e0174102

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Castalanelli MA, Teale R, Rix MG, Kennington WJ, Harvey MS (2014) Barcoding of mygalomorph spiders (Araneae: Mygalomorphae) in the Pilbara bioregion of Western Australia reveals a highly diverse biota. Invertebr Syst 28:375–385

    Article  CAS  Google Scholar 

  • Castalanelli MA, Huey JA, Hillyer MJ, Harvey MS (2017) Molecular and morphological evidence for a new genus of small trapdoor spiders from arid Western Australia (Araneae: Mygalomorphae: Nemesiidae: Anaminae). Invertebr Syst 31:492–505

    Article  Google Scholar 

  • Caterino MS, Cho S, Sperling FAH (2000) The current state of insect molecular systematics: a thriving tower of babel. Ann Rev Entomol 45:1–54

    Article  CAS  Google Scholar 

  • Chamberland L, McHugh A, Kechejian S, Binford GJ, Bond JE, Coddington J, Dolman G, Hamilton CA, Harvey MS, Kuntner M, Agnarsson I (2018) From Gondwana to GAARlandia: evolutionary history and biogeography of ogre-faced spiders (Deinopis). J Biogeogr 155:252–216

    Google Scholar 

  • Chen J, Zhao L, Jiang L, Meng E, Zhang Y, Xiong X, Liang S (2008) Transcriptome analysis revealed novel possible venom components and cellular processes of the tarantula Chilobrachys jingzhao venom gland. Toxicon 52:794–806

    Article  CAS  PubMed  Google Scholar 

  • Cheng D-Q, Piel WH (2018) The origins of the Psechridae: web-building lycosoid spiders. Mol Phylogenet Evol 125:213–219

    Article  PubMed  Google Scholar 

  • Clarke TH, Garb JE, Hayashi CY, Haney RA, Lancaster AK, Corbett S, Ayoub NA (2014) Multi-tissue transcriptomics of the black widow spider reveals expansions, co-options, and functional processes of the silk-gland gene toolkit. BMC Genomics 15:e365

    Article  CAS  Google Scholar 

  • Clarke TH, Garb JE, Hayashi CY, Arensburger P, Ayoub NA (2015) Spider transcriptomes identify ancient large-scale gene duplication event potentially important in silk gland evolution. Genome Biol Evol 7:1856–1870

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Coddington JA, Agnarsson I, Hamilton CA, Bond JE (2019) Spiders did not repeatedly gain, but repeatedly lost, foraging webs. PeerJ 7:e6703

    Article  PubMed  PubMed Central  Google Scholar 

  • Colgan DJ, McLauchlan A, Wilson GDF, Livingston SP, Edgecombe GD, Macarans J, Cassis G, Gray MR (1998) Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Aust J Zool 46:419–437

    Article  Google Scholar 

  • Cooper SJB, Harvey MS, Saint KM, Main BY (2011) Deep phylogeographic structuring of populations of the trapdoor spider Moggridgea tingle (Migidae) from southwestern Australia: evidence for long-term refugia within refugia. Mol Ecol 20:3219–3236

    Article  PubMed  Google Scholar 

  • Corzo G, Escoubas P (2003) Pharmacologically active spider peptide toxins. Cell Mol Life Sci 60:2409–2426

    Article  CAS  PubMed  Google Scholar 

  • Corzo G, Diego-García E, Clement H, Peigneur S, Odell G, Tytgat J, Possani LD, Alagón A (2008) An insecticidal peptide from the theraposid [sic] Brachypelma smithi spider venom reveals common molecular features among spider species from different genera. Peptides 29:1901–1908

    Article  CAS  PubMed  Google Scholar 

  • Crampton-Platt A, Yu DW, Zhou X, Vogler AP (2016) Mitochondrial metagenomics: letting the genes out of the bottle. GigaScience 5:e15

    Google Scholar 

  • Croom HB, Gillespie RG, Palumbi SR (1991) Mitochondrial DNA sequences coding for a portion of the RNA of the small ribosomal subunits of Tetragnatha mandibulata and Tetragnatha hawaiensis (Araneae, Tetragnathidae). J Arachnol 19:210–214

    Google Scholar 

  • Diego-García E, Peigneur S, Waelkens E, Debaveye S, Tytgat J (2010) Venom components from Citharischius crawshayi spider (Family Theraphosidae): exploring transcriptome, venomics, and function. Cell Mol Life Sci 67:2799–2813

    Article  PubMed  CAS  Google Scholar 

  • Dimitrov D, Benavides LR, Arnedo MA, Giribet G, Griswold CE, Scharff N, Hormiga G (2017) Rounding up the usual suspects: a standard target-gene approach for resolving the interfamilial phylogenetic relationships of ecribellate orb-weaving spiders with a new family-rank classification (Araneae, Araneoidea). Cladistics 33:221–250

    Article  PubMed  Google Scholar 

  • Edwards S, Liu L, Pearl D (2007) High-resolution species trees without concatenation. PNAS 104:5936–5941

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Faircloth BC (2017) Identifying conserved genomic elements and designing universal probe sets to enrich them. Mol Ecol Resour 8:1103–1112

    Google Scholar 

  • Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC (2012) Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst Biol 61:717–726

    Article  PubMed  Google Scholar 

  • Fang W-Y, Wang Z-L, Li C, Yang X-Q, Yu X-P (2016) The complete mitogenome of a jumping spider Carrhotus xanthogramma (Araneae: Salticidae) and comparative analysis in four salticid mitogenomes. Genetica 144:699–709

    Article  CAS  PubMed  Google Scholar 

  • Fernández R, Hormiga G, Giribet G (2014) Phylogenomic analysis of spiders reveals nonmonophyly of orb weavers. Curr Biol 24:1772–1777

    Article  PubMed  CAS  Google Scholar 

  • Fernández R, Kallal RJ, Dimitrov D, Ballesteros JA, Arnedo MA, Giribet G, Hormiga G (2018) Phylogenomics, diversification dynamics, and comparative transcriptomics across the spider tree of life. Curr Biol 28:1489–1497

    Article  PubMed  CAS  Google Scholar 

  • Field KG, Olsen GJ, Lane DJ, Giovannoni SJ, Ghiselin MT, Raff EC, Pace NR, Raff RA (1988) Molecular phylogeny of the animal kingdom. Science 239:748–753

    Article  CAS  PubMed  Google Scholar 

  • Foley S, Lüddecke T, Cheng D-Q, Krehenwinkel H, Künzel S, Longhorn SJ, Wendt I, von Wirth V, Tänzler R, Vences M, Piel WH (2019) Tarantula phylogenomics: a robust phylogeny of deep theraphosid clades inferred from transcriptome data sheds light on the prickly issue of urticating setae evolution. Mol Phylogenet Evol. 140:106573

    Article  PubMed  Google Scholar 

  • Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotech 3:294–299

    CAS  Google Scholar 

  • Foster PG, Hickey DA (1999) Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J Mol Evol 48:284–290

    Article  CAS  PubMed  Google Scholar 

  • French AS, Li AW, Meisner S, Torkkeli PH (2014) Upstream open reading frames and Kozak regions of assembled transcriptome sequences from the spider Cupiennius salei. Selection or chance? Gene 539:03–208

    Article  CAS  Google Scholar 

  • Frías-López C, Almeida FC, Guirao-Rico S, Vizueta J, Sánchez-Gracia A, Arnedo MA, Rozas J (2015) Comparative analysis of tissue-specific transcriptomes in the funnel-web spidr Macrothele calpeiana (Araneae, Hexathelidae). PeerJ 3:e1064

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Friedrich M, Tautz D (1995) Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature 376:165–167

    Article  CAS  PubMed  Google Scholar 

  • Fukushima CS, Bertani R (2017) Taxonomic revision and cladistic analysis of Avicularia Lamarck, 1818 (Araneae, Theraphosidae, Aviculariinae) with description of three new Aviculariine genera. ZooKeys 659:1–185

    Article  Google Scholar 

  • Garb JE, Shara PP, Ayoub NA (2018) Recent progress and prospects for advancing arachnid genomics. Curr Opin Insect Sci 25:51–57

    Article  PubMed  Google Scholar 

  • Garrison NL, Rodriquez J, Agnarsson I, Coddington JA, Griswold CE, Hamilton CA, Hedin M, Kocot KM, Ledford JM, Bond JE (2016) Spider phylogenomics: untangling the spider tree of life. PeerJ 4:e1719

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gillespie RG, Croom HB, Palumbi SR (1994) Multiple origins of a spider radiation in Hawaii. PNAS 91:2290–2294

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Godwin RL, Opatova V, Garrison NL, Hamilton CA, Bond JE (2018) Phylogeny of a cosmopolitan family of morphologically conserved trapdoor spiders (Mygalomorphae, Ctenizidae) using Anchored Hybrid Enrichment, with a description of the family, Haloproctidae Pocock 1901. Mol Phylogenet Evol 126:303–313

    Article  PubMed  Google Scholar 

  • Graham MR, Hendrixson BE, Hamilton CA, Bond JE (2015) Miocene extensional tectonics explain ancient patterns of diversification among turret-building tarantulas (Aphonopelma mojave) group in the Mojave and Sonoran deserts. J Biogeogr 42:1052–1065

    Article  Google Scholar 

  • Grbic M, Van Leeuwen T, Clark RM, Rombauts S, Rouze P, Grbic V, Osborne EJ, Dermauw W, Ngoc PC, Ortego F et al (2011) The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479:487–492

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gregory TR, Shorthouse DP (2003) Genome sizes of spiders. J Hered 94:285–290

    Article  CAS  PubMed  Google Scholar 

  • Guadanucci JPL (2014) Theraphosidae phylogeny: relationships of the ‘Ischnocolinae’ genera (Araneae, Mygalomorphae). Zool Scr 43:508–518

    Article  Google Scholar 

  • Guadanucci JPL, Wendt I (2014) Revision of the spider genus Ischnocolus Ausserer, 1871 (Mygalomorphae: Theraphosidae: Ischnocolinae). J Nat Hist 48(7–8):387–402

    Article  Google Scholar 

  • Hamilton CA, Formanowicz DR, Bond JE (2011) Species delimitation and phylogeography of Aphonopelma hentzi (Araneae, Mygalomorphae, Theraphosidae): cryptic diversity in North American tarantulas. PLoS One 6:e26207

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hamilton CA, Hendrixson BE, Brewer MS, Bond JE (2014) An evaluation of sampling effects on multiple DNA barcoding methods leads to an integrative approach for delimiting species: a case study of the North American tarantula genus Aphonopelma (Araneae, Mygalomorphae, Theraphosidae). Mol Phylogenet Evol 71:79–93

    Article  CAS  PubMed  Google Scholar 

  • Hamilton CA, Hendrixson BE, Bond JE (2016a) Taxonomic revision of the tarantula genus Aphonopelma Pocock, 1901 (Araneae, Mygalomorphae, Theraphosidae) within the United States. ZooKeys 560:1–340

    Article  Google Scholar 

  • Hamilton CA, Lemmon AR, Lemmon EM, Bond JE (2016b) Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life. BMC Evol Biol 16:e212

    Article  Google Scholar 

  • Haney RA, Ayoub NA, Clarke TH, Hayashi CY, Garb JE (2014) Dramatic expansion of the black widow toxin arsenal uncovered by multi-tissue transcriptomics and venom proteomics. BMC Genomics 15:e366

    Article  CAS  Google Scholar 

  • Harrison SE, Harvey MS, Cooper SJB, Austin AD, Rix MG (2017) Across the Indian Ocean: a remarkable example of trans-oceanic dispersal in an austral mygalomorph spider. PLoS One 12(8):e0180139

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Harrison SE, Rix MG, Harvey MS, Austin AD (2018) Systematics of the Australian spiny trapdoor spiders of the genus Blakistonia Hogg (Araneae: Idiopidae). Zootaxa 4518:001–076

    Article  Google Scholar 

  • Harvey MS, Hillyer MJ, Main BY, Moulds TA, Raven RJ, Rix MG, Vink CJ, Huey JA (2018) Phylogenetic relationships of the Australian 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 184:407–452

    Article  Google Scholar 

  • Hassanin A (2006) Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution. Mol Phylogenet Evol 38:100–116

    Article  CAS  PubMed  Google Scholar 

  • Hassanin A, Léger N, Deutsch J (2005) Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences. Syst Biol 54:277–298

    Article  PubMed  Google Scholar 

  • Hausdorf B (1999) Molecular phylogeny of araneomorph spiders. J Evol Biol 12:980–985

    Article  CAS  Google Scholar 

  • Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003a) Biological identifications through DNA barcodes. P R Soc Lond Ser B Biol Sci 270:313–321

    Article  CAS  Google Scholar 

  • Hebert PDN, Ratnasingham S, de Waard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. P R Soc Lond Ser B Biol Sci 270:S96–S99

    CAS  Google Scholar 

  • Hedin M, Bond JE (2006) Molecular phylogenetics of the spider infraorder Mygalomorphae using nuclear rRNA genes (18S and 28S): conflict and agreement with the current system of classification. Mol Phylogenet Evol 41:454–471

    Article  CAS  PubMed  Google Scholar 

  • Hedin M, Carlson D (2011) A new trapdoor spider species from the southern coast ranges of California (Mygalomorphae, Antrodiaetidae, Aliatypus coylei, sp. nov,) including consideration of mitochondrial phylogeographic structuring. Zootaxa 2963:55–68

    Article  Google Scholar 

  • Hedin MC, Maddison WP (2001) A combined molecular approach to phylogeny of the jumping spider subfamily Dendryphantinae (Araneae: Salticidae). Mol Phylogenet Evol 18(3):386–403

    Article  CAS  PubMed  Google Scholar 

  • Hedin M, Starrett J, Hayashi C (2013) Crossing the uncrossable: novel trans-valley biogeographic patterns revealed in the genetic history of low-dispersal mygalomorph spiders (Antrodiaetidae, Antrodiaetus) from California. Mol Ecol 22:508–526

    Article  CAS  PubMed  Google Scholar 

  • Hedin M, Carlson D, Coyle F (2015) Sky island diversification meets the multispecies coalescent – divergence in the spruce-fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia. Mol Ecol 24:3467–3484

    Article  PubMed  Google Scholar 

  • Hedin M, Derkarabetian S, Ramirez MJ, Vink C, Bond JE (2018a) Phylogenomic reclassification of the world’s most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution. Nat Sci Rep 8:e1636

    Article  CAS  Google Scholar 

  • Hedin M, Derkarabetian S, Blair J, Paquin P (2018b) Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae). ZooKeys 769:49

    Article  Google Scholar 

  • Hedin M, Derkarabetian S, Alfaro A, Ramírez MJ, Bond JE (2019) Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci. PeerJ 7:e6864

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hendriks L, Huysmans E, Vandenberghe A, De Wachter R (1986) Primary structures of the 5S ribosomal RNAs of 11 arthropods and applicability of 5S RNA to the study of metazoan evolution. J Mol Evol 24:103–109

    Article  CAS  Google Scholar 

  • Hendriks L, Van Broeckhoven C, Vandenberghe A, Van de Peer Y, De Wachter R (1988) Primary and Secondary Structure of the 18S ribosomal RNA of the bird spider Eurypelma californica and evolutionary relationships among eukaryotic phyla. Eur J Biochem 177:15–20

    Article  CAS  PubMed  Google Scholar 

  • Hendrixson BE, Bond JE (2005) Testing species boundaries in the Antrodiaetus unicolor complex (Araneae: Mygalomorphae: Antrodiaetidae): “paraphyly” and cryptic diversity. Mol Phylogenet Evol 36:405–416

    Article  PubMed  Google Scholar 

  • Hendrixson BE, Bond JE (2007) Molecular phylogeny and biogeography of an ancient Holarctic lineage of mygalomorph spiders (Araneae: Antrodiaetidae: Antrodiaetus). Mol Phylogenet Evol 42:738–755

    Article  CAS  PubMed  Google Scholar 

  • Hendrixson BE, Bond JE (2009) Evaluating the efficacy of continuous quantitative characters for reconstructing the phylogeny of a morphologically homogeneous spider taxon (Araneae, Mygalomorphae, Antrodiaetidae, Antrodiaetus). Mol Phylogenet Evol 53:300–313

    Article  CAS  PubMed  Google Scholar 

  • Hendrixson BE, DeRussy BM, Hamilton CA, Bond JE (2013) An exploration of species boundaries in turret-building tarantulas of the Mojave Desert (Araneae, Mygalomorphae, Theraphosidae, Aphonopelma). Mol Phylogenet Evol 66:327–340

    Article  PubMed  Google Scholar 

  • Hendrixson E, Guice AV, Bond JE (2015) Integrative species delimitation and conservation of tarantulas (Araneae, Mygalomorphae, Theraphosidae) from a North American biodiversity hotspot. Insect Conser Diver 8:120–131

    Article  Google Scholar 

  • Herzig V, King GF, Undheim EAB (2019) Can we resolve the taxonomic bias in spider venom research? Toxicon 1:e100005

    Article  CAS  Google Scholar 

  • Huang H, He Q, Kubatko LS, Knowles LL (2010) Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. Syst Biol 59:573–583

    Article  PubMed  Google Scholar 

  • Huber KC, Haider THS, Muller MW, Huber BA, Schwayen RJ, Barth FG (1993) DNA sequence data indicates the polyphyly of the family Ctenidae (Araneae). J Arachnol 21:194–201

    Google Scholar 

  • Hughes J, Longhorn SJ, Papadopoulou A, Theodorides K, de Riva A, Meija-Chang M, Foster PG, Vogler AP (2006) Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (Beetles). Mol Biol Evol 23:268–278

    Google Scholar 

  • Hüsser M (2018) A first phylogenetic analysis reveals a new arboreal tarantula genus from South America with description of a new species and two new species of Tapinauchenius Ausserer, 1871 (Araneae, Mygalomorphae, Theraphosidae). ZooKeys 784:59–93

    Article  Google Scholar 

  • Huysmans E, Dams E, Vandenberghe A, De Wachter R (1983) The nucleotide sequences of the 5S rRNA of four mushrooms and their use in studying the phylogenetic position of basidiomycetes among the eukaryotes. Nucleic Acids Res 11:2871–2879

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hwang UW, Park CJ, Yong TS, Kim W (2001) One-step PCR amplification of complete arthropod mitochondrial genomes. Mol Phylogenet Evol 26:110–120

    Google Scholar 

  • i5K Consortium (2013) The i5K initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment. J Hered 104:595–600

    Article  PubMed Central  Google Scholar 

  • Jiang L, Zhang D, Zhang Y, Peng L, Chen J, Liang S (2010) Venomics of the spider Ornithoctonus huwena based on transcriptomic versus proteomic analysis. Comp Biochem Physiol D 5:81–88

    Google Scholar 

  • Kallal RJ, Fernández R, Giribet G, Hormiga G (2018) A phylotranscriptomic backbone of the orb-weaving spider family Araneidae (Arachnida, Araneae) supported by multiple methodological approaches. Mol Phylogenet Evol 126:129–140

    Article  PubMed  Google Scholar 

  • Kocher TD, Thomas WK, Meyer A, Edwards SV, Paabo S, Villablanca FX (1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. PNAS 86:6196–6200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kono N, Nakamura H, Ohtoshi R, Pedrazzoli-Moran DA, Shinohara A, Yoshida Y, Fujiwara M, Mori M, Tomita M, Arakawa K (2019) Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue. Sci Rep 9:e8380

    Article  CAS  Google Scholar 

  • Kornilios P, Thanou E, Kapli P, Parmakelis A, Chatzaki M (2016) Peeking through the trapdoor: historical biogeography of the Aegean endemic spider Cyrtocarenum Ausserer, 1871 with an estimation of mtDNA substitution rates for Mygalomorphae. Mol Phylogenet Evol 98:300–313

    Article  CAS  PubMed  Google Scholar 

  • Král J, Kořínková T, Krkavcová L, Musilová J, Forman M, Ávila Herrera IM, Haddad CR, Vítková M, Henriques S, Palacios Vargas JG, Hedin M (2013) Evolution of karyotype, sex chromosomes, and meiosis in mygalomorph spiders (Araneae: Mygalomorphae). Biol J Linn Soc 109:377–408

    Article  Google Scholar 

  • Krehenwinkel H, Kennedy SR, Rueda A, Lam A, Gillespie RG (2018) Scaling up DNA barcoding – primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing. Methods Ecol Evol 9:2181–2193

    Article  Google Scholar 

  • Krehenwinkel H, Pomerantz A, Henderson JB, Kennedy SR, Lim JY, Swamy V, Shoobridge JD, Patel NH, Gillespie RG, Prost S (2019) Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale. GigaScience 8:giz006

    Google Scholar 

  • Kriventseva EV, Kuznetsov D, Tegenfeldt F, Manni M, Dias R, Simão FA, Zdobnov EM (2019) OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. Nucleic Acids Res 47:D807–D811

    Article  CAS  PubMed  Google Scholar 

  • Kuntner M, Agnarsson I (2011) Biogeography and diversification of hermit spiders on Indian Ocean islands (Nephilidae: Nephilengys). Mol Phylogenet Evol 59:477–488

    Article  PubMed  Google Scholar 

  • Kuntner M, Hamilton CA, Cheng R-C, Gregorič M, Lupše N, Lemmon EM, Lemmon AR, Agnarsson I, Coddington JA, Bond JE (2019) Golden orbweavers ignore biological rules: phylogenomic and comparative analyses unravel a complex evolution of sexual size dimorphism. Syst Biol 68:555–572

    Article  PubMed  Google Scholar 

  • Leaché AD, Rannala B (2011) The accuracy of species tree estimation under simulation: a comparison of methods. Syst Biol 60:126–137

    Article  PubMed  Google Scholar 

  • Leavitt DH, Starrett J, Westphal MF, Hedin M (2015) Multilocus sequence data reveals dozens of putative cryptic species in a radiation of endemic Californian mygalomoprph spiders (Araneae, Mygalomorphae, Nemesiidae). Mol Phylogenet Evol 91:56–67

    Article  PubMed  Google Scholar 

  • Lemmon AR, Emme SA, Lemmon EM (2012) Anchored Hybrid Enrichment for massively high-throughput phylogenomics. Syst Biol 61:727–744

    Article  CAS  PubMed  Google Scholar 

  • Lewin HA, Robinson GE, Kress WJ et al (2018) Earth BioGenome Project: sequencing life for the future of life. PNAS 17:4325–4333

    Article  CAS  Google Scholar 

  • Liu L, Yu L (2011) Estimating species trees from unrooted gene trees. Syst Biol 60:661–667

    Article  PubMed  Google Scholar 

  • Liu M, Zhang Z, Peng Z (2015) The mitochondrial genome of the water spider Argyroneta aquatica (Araneae: Cybaeidae). Zool Scr 44:179–190

    Article  Google Scholar 

  • Liu S, Wang X, Xie L, Tan M, Li Z, Su X, Zhang H, Misof B, Kjer KM, Tang M, Niehuis O, Jiang H, Zhou X (2016) Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis. Mol Ecol Resour 16:470–479

    Article  CAS  PubMed  Google Scholar 

  • Longhorn SJ, Nicholas M, Chuter J, Vogler AP (2007) The utility of molecular markers from non-lethal DNA samples of the CITES II protected “tarantula” Brachypelma vagans (Araneae, Theraphosidae). J Arachnol 35:278–292

    Article  Google Scholar 

  • Lopardo L, Uhl G (2014) Testing mitochondrial marker efficacy for DNA barcoding in spiders: a test case using the dwarf spider genus Oedothorax (Araneae: Linyphiidae: Erigoninae). Invertebr Syst 28:501–521

    Article  CAS  Google Scholar 

  • Lorenzini DM, da Silva PI, Soares MB, Arruda P, Setubal J, Daffre S (2006) Discovery of immune-related genes expressed in hemocytes of the tarantula spider Acanthoscurria gomesiana. Dev Comp Immun 30:545–556

    Article  CAS  Google Scholar 

  • Lüddecke T, Krehenwinkel H, Canning G, Glaw F, Longhorn SJ, Tänzler R, Wendt I, Vences M (2018) Discovering the silk road: nuclear and mitochondrial sequence data resolve the phylogenetic relationships among theraphosid spider subfamilies. Mol Phylogenet Evol 119:63–70

    Article  PubMed  Google Scholar 

  • Macher JK, Zizka V, Weigand AM, Leese F (2018) A simple centrifugation protocol for metagenomic studies increases mitochondrial DNA yield by two orders of magnitude. Methods Ecol Evol 9:1070–1074

    Article  Google Scholar 

  • Maddison WP, Hedin MC (2003) Jumping spider phylogeny (Araneae: Salticidae). Invertebr Syst 17:529–549

    Article  Google Scholar 

  • Maddison W, Knowles L (2006) Inferring phylogeny despite incomplete lineage sorting. Syst Biol 55:21–30

    Article  PubMed  Google Scholar 

  • Maddison WP, Evans SC, Hamilton CA, Bond JE, Lemmon AR, Lemmon EM (2017) A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment. ZooKeys 89:89–101

    Article  Google Scholar 

  • Masta SE, Boore JL (2004) The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs. Mol Biol Evol 21:893–902

    Article  CAS  PubMed  Google Scholar 

  • Masta SE, Boore JL (2008) Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomes. Mol Biol Evol 25:949–959

    Article  CAS  PubMed  Google Scholar 

  • Masta SE, Longhorn SJ, Boore JL (2009) Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analyses. Mol Phylogenet Evol 50:117–128

    Article  CAS  PubMed  Google Scholar 

  • Masta SE, McCall A, Longhorn SJ (2010) Rare genomic changes and mitochondrial sequences provide independent support for congruent relationships among the sea spiders (Arthropoda, Pycnogonida). Mol Phylogenet Evol 57:59–70

    Article  CAS  PubMed  Google Scholar 

  • Mendoza J, Francke O (2017) Systematic revision of Brachypelma red-kneed tarantulas (Araneae: Theraphosidae), and the use of DNA barcodes to assist in the identification and conservation of CITES-listed species. Invertebr Syst 31:157–179

    Article  Google Scholar 

  • Meng X, Zhang Y, Bao H, Liu Z (2015) Sequence analysis of insecticide action and detoxification-related genes in the insect pest natural enemy Pardosa pseudoannulata. PLoS One 10:e0125242

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mikheyev AS, Zwick A, Magrath MJL, Grau ML, Qiu L, Su YN, Yeates D (2017) Museum genomics confirms that the Lord Howe Island stick insect survived extinction. CURBIO 27:3157–3161.e4

    CAS  Google Scholar 

  • Miller JA, Beentjes KK, van Helsdingen P, Ijland S (2013) Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol. ZooKeys 365:245–261

    Article  Google Scholar 

  • Mirza Z, Sanap RV, Bhosale H (2014) Preliminary review of Indian Eumenophorinae (Araneae: Theraphosidae) with description of a new genus and five new species from the Western Ghats. PLoS One 9:e87928

    Google Scholar 

  • Montes de Oca L, D’Elía G, Pérez-Miles F (2016) An integrative approach for species delimitation in the spider genus Grammostola (Theraphosidae, Mygalomorphae). Zool Scr 45:322–333

    Article  Google Scholar 

  • Mora E, Paspati A, Decae AE, Arnedo MA (2017) Rafting spiders or drifting islands? Origins and diversification of the endemic trap-door spiders from the Balearic Islands, Western Mediterranean. J Biogeogr 44:924–936

    Article  Google Scholar 

  • Moritz C, Dowling TE, Brown WM (1987) Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Ann Rev Ecol Syst 18:269–292

    Article  Google Scholar 

  • Mullis KB, Faloona FA (1987) Specific synthesis of DNA in vitro via a polymerase catalyzed chain reaction. Method Enzymol 155:335–350

    Article  CAS  Google Scholar 

  • Nentwig W (2012) The species referred to as Eurypelma californicum (Theraphosidae) in more than 100 publications is likely to be Aphonopelma hentzi. J Arachnol 40:128–130

    Article  Google Scholar 

  • Opatova V, Arnedo MA (2014a) Spiders on a hot volcanic roof: colonisation pathways and phylogeography of the Canary Islands endemic trap-door spider Titanidiops canariensis (Araneae, Idiopidae). PLoS One 9:e115078

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Opatova V, Arnedo MA (2014b) From Gondwana to Europe: inferring the origins of Mediteranean Macrothele spiders (Araneae: Hexathelidae) and the limits of the faily Hexathelidae. Invertebr Syst 28:361–374

    Article  Google Scholar 

  • Opatova V, Bond JE, Arnedo MA (2013) Ancient origins of the Mediterranean trap-door spiders of the family Ctenizidae (Araneae, Mygalomorphae). Mol Phylogenet Evol 69:1135–1145

    Article  PubMed  Google Scholar 

  • Opatova V, Bond JE, Arnedo MA (2016) Uncovering the role of the Western Mediterranean tectonics in shaping the diversity and distribution of the trap-door spider genus Ummidia (Araneae, Ctenizidae). J Biogeogr 43:1955–1966

    Article  Google Scholar 

  • Opatova V, Hamilton CH, Hedin M, Montes de Oca L, Král J, Bond JE (2019) Phylogenetic systematics and evolution of the spider infraorder Mygalomorphae using genomic scale data. Systematic Biology 69:671–707

    Google Scholar 

  • Ortiz D, Francke OF (2016) Two DNA barcodes and morphology for multi-method species delimitation in Bonnetina tarantulas (Araneae: Theraphosidae). Mol Phylogenet Evol 101:176–193

    Article  CAS  PubMed  Google Scholar 

  • Ortiz D, Francke OF (2017) Reconciling morphological an molecular systematics in tarantulas (Araneae: Theraphosidae): revision of the Mexican endemic genus Bonnetina. Zool J Linn Soc 180(4):819–886

    Article  Google Scholar 

  • Ortiz D, Francke OF, Bond JE (2018) A tangle of forms and phylogeny: extensive morphological homoplasy and molecular clock heterogeneity in Bonnetina and related tarantulas. Mol Phylogenet Evol 127:55–73

    Article  CAS  PubMed  Google Scholar 

  • Parra G, Bradnam K, Ning Z, Keane T, Korf I (2009) Assessing the gene space in draft genomes. Nucleic Acids Res 37:289–297

    Article  CAS  PubMed  Google Scholar 

  • Perafán C, Galvis W, Gutiérrez M, Pérez-Miles F (2016) Kankuamo, a new theraphosid genus from Colombia (Araneae, Mygalomorphae), with a new type of urticating setae and divergent male genitalia. ZooKeys 601:89–109

    Article  Google Scholar 

  • Pérez-Miles F (1998) Notes on the systematics of the little known theraphosid spider Hemirrhagus cervinus, with a description of a new type of urticating hair. J Arachnol 26:120–123

    Google Scholar 

  • Petersen SD, Mason T, Akber S, West R, White B, Wilson P (2007) Species identification of tarantulas using exuviae for international wildlife law enforcement. Conserv Genet 8:497–502

    Article  Google Scholar 

  • Podsiadlowski L, Arabi J and Fahrein K (Unpublished) Mitochondrial genomes of three spider species. Genbank submission 31 Jan 2013

    Google Scholar 

  • Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, Sumlin WD, Vogler AP (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol 55:595–609

    Article  PubMed  Google Scholar 

  • Qiu Y, Song D, Zhou K, Sun H (2005) The mitochondrial sequences of Heptethela hangzhouensis and Ornithoctonus huwena reveal unique gene arrangements and atypical tRNAs. J Mol Evol 60:57–71

    Article  CAS  PubMed  Google Scholar 

  • Regier JC, Schultz JW (1997) Molecular phylogeny of the major arthropod Groups indicates Polyphyly of Crustaceans and a new hypothesis for the origins of Hexapods. Mol Biol Evol 14:902–913

    Article  CAS  PubMed  Google Scholar 

  • Richards S (2015) It’s more than stamp collecting: how genome sequencing can unify biological research. Trends Genet 31:411–421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rix MG, Cooper SJB, Meusemann K, Klopfstein S, Harrison SE, Harvey MS (2017a) Post-Eocene climate change across continental Australia and the diversification of Australasian spiny trapdoor spiders (Idiopidae: Arbanitinae). Mol Phylogenet Evol 109:302–320

    Article  PubMed  Google Scholar 

  • Rix MG, Bain K, Main BY, Raven RJ, Austin AD, Cooper SJB (2017b) Systematics of the spiny trapdoor spiders of the genus Cataxia (Mygalomorphae: Idiopidae) from south-western Australia: documenting a threatened fauna in a sky-island landscape. J Arachnol 45:395–423

    Article  Google Scholar 

  • Rix MG, Raven RJ, Harvey MS (2018a) Systematics of the giant trapdoor spiders of the genus Gaius Rainbow (Mygalomorphae: Idiopidae: Aganippini): documenting an iconic lineage of the Western Australian inland arid zone. J Arachnol 46:438–472

    Article  Google Scholar 

  • Rix MG, Raven RJ, Austin AD, Cooper SJB, Harvey MS (2018b) Systematics of the spiny trapdoor spider genus Bungulla (Mygalomorphae: Idiopidae): revealing a remarkable radiation of mygalomorph spiders from the Western Australian arid zone. J Arachnol 46:249–344

    Article  Google Scholar 

  • Robinson AE, Blagoev G, Hebert P, Adamowicz SJ (2009) Prospects for using DNA barcoding to identify spiders in species-rich genera. ZooKeys 16:27–46

    Article  Google Scholar 

  • Roehrdanz RL (1995) Amplification of complete insect mitochondrial genome in two easy pieces. Insect Mol Biol 4:169–172

    Article  CAS  PubMed  Google Scholar 

  • Ruane S, Austin CC (2017) Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens. Mol Ecol Resour 17:1003–1008

    Article  PubMed  Google Scholar 

  • Sanger F, Coulson AR (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94:441–448

    Article  CAS  PubMed  Google Scholar 

  • Sanggaard KW, Bechsgaard JS, Fang X, Duan J, Dyrlund TF, Gupta V, Jiang X, Cheng L, Fan D, Feng Y, Han L, Huang Z, Wu Z, Liao L, Settepani V, Thøgersen IB, Vanthournout B, Wang T, Zhu Y, Funch P, Enghild JJ, Schauser L, Andersen SU, Villesen P, Schierup MH, Bilde T, Wang J (2014) Spider genomes provide insight into composition and evolution of venom and silk. Nat Commun 5:1–11

    Google Scholar 

  • Satler JD, Starrett J, Hayashi CY, Hedin M (2011) Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiatidae, Aliatypus). PLoS One 6:e25355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Satler JD, Carstens BC, Hedin M (2013) Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiatidae, Aliatypus). Syst Biol 62:805–823

    Article  PubMed  Google Scholar 

  • Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T et al (2017) The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 15:e62

    Article  CAS  Google Scholar 

  • Sharma PP, Kaluziak ST, Perez-Porro AR, Gonzalez VL, Hormiga G, Wheeler WC, Giribet G (2014) Phylogenomic interrogation of Arachnida reveals systemic conflicts in phylogenetic signal. Mol Biol Evol 31:2963–2984

    Article  CAS  PubMed  Google Scholar 

  • Shokralla S, Porter TM, Gibson JF, Dobosz R, Janzen DH, Hallwachs W, Golding GB, Hajibabaei M (2015) Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Sci Rep 5:9687

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212

    Article  PubMed  CAS  Google Scholar 

  • Simon C, Frati F, Beckenbach A, Crespi B, Liu H, Flook P (1994) Evolution, weighting and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann Entomol Soc Amer 87:651–701

    Article  CAS  Google Scholar 

  • Simon C, Buckley TR, Frati F, Stewart JB, Beckenbach AT (2006) Incorporating molecular evolution into phylogenetic analyses, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Ann Rev Ecol Evol Syst 37:545–579

    Article  Google Scholar 

  • Smith SD, Bond JE (2003) An analysis of the secondary structure of the mitochondrial large subunit rRNA gene (16S) in spiders and its implications for phylogenetic reconstructions. J Arachnol 31:44–54

    Article  Google Scholar 

  • Smith BT, Harvey MG, Faircloth BC, Glenn TC, Brumfield RT (2014) Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Syst Biol 63:83–95

    Article  PubMed  Google Scholar 

  • Spagna JC, Gillespie RG (2008) More data, fewer shifts: molecular insights into the evolution of the spinning apparatus in non-orb-weaving spiders. Mol Phylogenet Evol 46:347–368

    Article  PubMed  Google Scholar 

  • Srivathsan A, Baloğlu B, Wang W, Tan WX, Bertrand D, AHQ N, EJH B, JJY K, Nagarajan N, Meier R (2018) A MinION(tm)-based pipeline for fast and cost-effective DNA barcoding. Mol Ecol Resour 18:1035–1049

    Article  CAS  Google Scholar 

  • St Laurent RA, Hamilton CA, Kawahara AY (2018) Museum specimens provide phylogenomic data to resolve relationships of sack-bearer moths (Lepidoptera, Mimallonoidea, Mimallonidae). Syst Entomol 43:729–761

    Article  Google Scholar 

  • Starrett J, Hedin M (2007) Multilocus genealogies reveal multiple cryptic species and biogeographical complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodiaetidae). Mol Ecol 16:583–604

    Article  PubMed  Google Scholar 

  • Starrett J, Derkarabetian S, Hedin M, Bryson RW, McCormack JE, Faircloth BC (2017) High phylogenetic utility of an ultraconserved element probe set designed for Arachnida. Mol Ecol Resour 17:812–823

    Article  CAS  PubMed  Google Scholar 

  • Starrett J, Hayashi CY, Derkarabetian S, Hedin M (2018) Cryptic elevational zonation in trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus janus complex) from the California southern Sierra Nevada. Mol Phylogenet Evol 118:403–413

    Article  PubMed  Google Scholar 

  • Stockman AK, Bond JE (2007) Delimiting cohesion species: extreme population structuring and the role of ecological interchangeability. Mol Ecol 16:3374–3392

    Article  CAS  PubMed  Google Scholar 

  • Straub SCK, Parks M, Writemier K, Fishbein M, Cronn RC, Liston A (2012) Navigating the tip of the genoic iceberg: next-genetation sequencing for plant systematics. Am J Botany 99:349–364

    Article  CAS  Google Scholar 

  • Tang M, Tan M, Meng G, Yang S, Liu S, Song W, Li Y, Wu Q, Zhang A, Zhou X (2014) Multiplex sequencing of pooled mitochondrial genomes-a crucial step toward biodiversity analysis using mito-metagenomics. Nucleic Acids Res 42:e166

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tautz D, Arctander P, Minelli A, Thomas RH, Voger AP (2002) DNA points the way ahead in taxonomy. Nature 418:479

    Article  CAS  PubMed  Google Scholar 

  • Tautz D, Arctander P, Minelli A, Thomas RH, Voger AP (2003) A plea for DNA taxonomy. Trends Ecol Evol 18:70–74

    Article  Google Scholar 

  • Tian X-X, Pan W-J, Chen L-L, Xu Y-Y, Pan H-C (2016) The complete mitochondrial genome of stretch spider Tetragnatha maxillosa (Araneae: Tetragnathidae). Mitochondrial DNA A DNA Mapp Seq Anal 27:3469–3470

    CAS  PubMed  Google Scholar 

  • Tilak M-K, Justy F, Debiais-Thibaud M, Botero-Castro F, Delsuc F, Douzery EJP (2015) A cost-effective straightforward protocol for shotgun Illumina libraries designed to assemble complete mitogenomes from non-model species. Conserv Genet Resour 7:37–40

    Article  Google Scholar 

  • Timmermans MJTN, Dodsworth S, Culverwell CL, Bocak L, Ahrens D, Littlewood DT, Pons J, Vogler AP (2010) Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Res 38:e197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Timmermans MJTN, Viberg C, Martin G, Hopkins K, Vogler AP (2016) Rapid assembly of taxonomically validated mitochondrial genomes from historical insects collections. Biol J Linn Soc 117:83–95

    Article  Google Scholar 

  • Turbeville JM, Pfeifer DM, Field KG, Raff RA (1991) The phylogenetic status of arthropods as inferred from 18S rRNA sequences. Mol Biol Evol 8:669–686

    CAS  PubMed  Google Scholar 

  • Turner SP, Longhorn SJ, Hamilton CA, Gabriel R, Pérez-Miles F, Vogler AP (2018) Re-evaluating conservation priorities of New World tarantulas (Araneae: Theraphosidae) in a molecular framework indicates non-monophyly of the genera, Aphonopelma and Brachypelma. Syst Biodiv 16:89–107

    Article  Google Scholar 

  • Undheim EAB, Sunagar K, Herzig V, Kely L, Low DHW, Jackson TNW, Jones A, Kurniawan N, King GF, Ali SA, Antunes A, Ruder T, Fry BG (2013) A proteomics and transcriptomics investigation of the venom from the barychelid spider Trittame loki (Brush-foot trapdoor). Toxins 5:2488–2503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van Dam MH, Lam AW, Sagata K, Gewa B, Laufa R, Balke M, Faircloth BC, Riedel A (2017) Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils. PLoS One 12:e0188044

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wang Z-L, Li C, Fang W-Y, Yu X-P (2016a) The complete mitochondrial genome of two Tetragnatha spiders (Araneae: Tetragnathidae): severe truncation of tRNAs and novel gene rearrangements in Araneae. Int J Biol Sci 12:109–119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Z-L, Li C, Fang WY, Yu XP (2016b) Characterization of the complete mitogenomes of two Neoscona spiders (Araneae: Araneidae) and its phylogenetic implications. Gene 590:298–306

    Article  CAS  PubMed  Google Scholar 

  • Waterhouse RM, Seppey M, Simão FA, Manni M, Ioannidis P, Klioutchnikov G, Kriventseva EV, Zdobnov EM (2018) BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol 35:543–548

    Article  CAS  PubMed  Google Scholar 

  • West RC, Marshall SD, Fukushima CS, Bertani R (2008) Review and cladistic analysis of the Neotropical tarantula genus Ephebopus Simon 1892 (Araneae: Theraphosidae) with notes on the Aviculariinae. Zootaxa 1849:35–58

    Article  Google Scholar 

  • Wheeler WC, Hayashi CY (1998) The phylogeny of extant Chelicerate orders. Cladistics 14:173–192

    Article  PubMed  Google Scholar 

  • Wheeler WC, Cartwright P, Hayashi CY (1993) Arthropod phylogeny: a combined approach. Cladistics 9:1–39

    Article  PubMed  Google Scholar 

  • Wheeler WC, Coddington JA, Crowley LM, Dimitrov D, Goloboff PA, Griswold CE, Hormiga G, Prendini L, Ramírez MJ, Sierwald P, Almeida-Silva L, Alvarez-Padilla F, Arnedo MA, Benavides Silva LR, Benjamin SP, Bond JE, Grismado CJ, Hasan E, Hedin M, Izquierdo MA, Labarque FM, Ledford J, Lopardo L, Maddison WP, Miller JA, Piacentini LN, Platnick NI, Polotow D, Silva-Dávila D, Scharff N, Szűts T, Ubick D, Vink CJ, Wood HM, Zhang J (2017) The spider tree of life: phylogeny of Araneae based on target-gene analyses from an extensive taxon sampling. Cladistics 33:574–616

    Article  PubMed  Google Scholar 

  • Wilson JS, Gunnell CF, Wahl DB, Pitts JP (2012) Testing the species limits of the tarantulas (Araneae: Theraphosidae) endemic to California’s southern coast ranges, USA. Insect Conserv Div 6:365–371

    Article  Google Scholar 

  • Wood HM, González VL, Lloyd M, Coddington J, Scharff N (2018) Next-Generation museum genomics: phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea). Mol Phylogenet Evol 127:907–918

    Article  CAS  PubMed  Google Scholar 

  • World Spider Catalog (2019) World Spider Catalog. Version 20.0. Natural History Museum, Bern. http://wsc.nmbe.ch. Accessed Jun 2019

  • Yu DW, Ji Y, Emerson BC, Wang X, Ye C, Yang C, Ding Z (2012) Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol Evol 3:613–623

    Article  Google Scholar 

  • Zhu J, Sun Y, Zhao F-Q, Yu J, Craig R, Hu S (2009) Analysis of tarantula skeletal muscle protein sequences and identification of transcriptional isoforms. BMC Genomics 10:e117

    Article  CAS  Google Scholar 

  • Zhu H-F, Wang Z-Y, Wang Z-L, Yu X-P (2019) Complete mitochondrial genome of the crab spider Ebrechtella tricuspidata (Araneae: Thomisidae): a novel tRNA rearrangement and phylogenetic implications for Araneae. Genomics 111:1266–1273

    Google Scholar 

  • Zuckerkandl E, Pauling L (1965) Molecules as documents of evolutionary history. J Theor Biol 8:357–366

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Brent Hendrixson for his insightful comments that greatly improved this chapter, and Fernando Pérez-Miles for the opportunity to provide this contribution. Chris Hamilton thanks Jason Bond for his guidance and mentorship during Hamilton’s PhD and partnership during development of Anchored Hybrid Enrichment in spiders. Stuart Longhorn thanks Alfried Vogler for mentorship during Longhorn’s formative years, as well as Susan Masta and Davide Pisani for later informative guidance.

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Longhorn, S.J., Hamilton, C.A. (2020). A Molecular Approach to the Phylogeny of Theraphosidae and Their Kin. In: Pérez-Miles, F. (eds) New World Tarantulas. Zoological Monographs, vol 6. Springer, Cham. https://doi.org/10.1007/978-3-030-48644-0_2

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