Bibliography
Adrián-Serrano, S., Lozano-Fernandez, J., Pons, J., Rozas, J., & Arnedo, M. A. (2021). On the shoulder of giants: Mitogenome recovery from non-targeted genome projects for phylogenetic inference and molecular evolution studies. Journal of Zoological Systematics and Evolutionary Research , 59 (1), 5–30. doi: 10.1111/jzs.12415
Arnedo, M. A., Oromí, P., Múrria, C., Macías-Hernández, N., & Ribera, C. (2007). The dark side of an island radiation: Systematics and evolution of troglobitic spiders of the genus Dysdera Latreille (Araneae:Dysderidae) in the Canary Islands. Invertebrate Systematics , 21 (6), 623–660. doi: 10.1071/IS07015
Arnedo, M. A., Oromí, P., & Ribera, C. (2001). Radiation of the spider genus Dysdera (Araneae, Dysderidae) in the Canary Islands: Cladistic assessment based on multiple data sets. Cladistics ,17 (4), 313–353. doi: 10.1006/clad.2001.0168
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., … & Sherlock, G. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics , 25 (1), 25–29.
Bleidorn, C. (2016). Third generation sequencing: technology and its potential impact on evolutionary biodiversity research.Systematics and Biodiversity , 14 (1), 1–8. doi: 10.1080/14772000.2015.1099575
Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M., & Borodovsky, M. (2021). BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genomics and Bioinformatics , 3 (1), 1–11. doi: 10.1093/nargab/lqaa108
Chan, P. P., Lin, B. Y., Mak, A. J., & Lowe, T. M. (2019). TRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes. BioRxiv , (6). doi: 10.1101/614032
Clifton, B. D., Jimenez, J., Kimura, A., Chahine, Z., Librado, P., Sanchez-Gracia, A., … Ranz, J. M. (2020). Understanding the early evolutionary stages of a tandem drosophila melanogaster -specific gene family: A structural and functional population study.Molecular Biology and Evolution , 37 (9), 2584–2600. doi: 10.1093/molbev/msaa109
Coddington, Jonathan A., Giribet, G., Harvey, M. S., Prendini, L., and Walter, D. E. (2004). “Arachnida.” in Assembling the Tree of Life.Oxford University Press , 296–318.
Croset, V., Rytz, R., Cummins, S. F., Budd, A., Brawand, D., Kaessmann, H., … Benton, R. (2010). Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction. PLoS Genetics , 6 (8). doi: 10.1371/journal.pgen.1001064
Eddy, S. R. (2011). Accelerated profile HMM searches. PLoS Computational Biology , 7 (10). doi: 10.1371/journal.pcbi.1002195
Fan, Z., Yuan, T., Liu, P., Wang, L.-Y., Jin, J.-F., Zhang, F., & Zhang, Z.-S. (2021). A chromosome-level genome of the spiderTrichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event .GigaScience , 10 (3), 1–15. doi: 10.1093/gigascience/giab016
Garb, J. E., Sharma, P. P., & Ayoub, N. A. (2018). Recent progress and prospects for advancing arachnid genomics. Current Opinion in Insect Science , 25 , 51–57. doi: 10.1016/j.cois.2017.11.005
Grbić, M., Van Leeuwen, T., Clark, R. M., Rombauts, S., Rouzé, P., Grbić, V., … Van De Peer, Y. (2011). The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature ,479 (7374), 487–492. doi: 10.1038/nature10640
Gu, Z., Eils, R., & Schlesner, M. (2016). Complex heatmaps reveal patterns and correlations in multidimensional genomic data.Bioinformatics , 32 (18), 2847–2849. doi: 10.1093/bioinformatics/btw313
Hoff, K. J., Lomsadze, A., Borodovsky, M., & Stanke, M. (2019). Whole-genome annotation with BRAKER. Methods in Molecular Biology , 1962 (0), 65–95. doi: 10.1007/978-1-4939-9173-0_5
Hopkin, S. P., & Martin, M. H. (1985). Assimilation of zinc, cadmium, lead, copper, and iron by the spider Dysdera crocata, a predator of woodlice. Bulletin of Environmental Contamination and Toxicology ,34 (1), 183–187. doi: 10.1007/BF01609722
Hu, J., Fan, J., Sun, Z., & Liu, S. (2020). NextPolish: A fast and efficient genome polishing tool for long-read assembly.Bioinformatics , 36 (7), 2253–2255. doi: 10.1093/bioinformatics/btz891
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992). The rapid generation of mutation data matrices from protein sequences.Bioinformatics , 8 (3), 275–282.
Jones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C., … Hunter, S. (2014). InterProScan 5: Genome-scale protein function classification. Bioinformatics , 30 (9), 1236–1240. doi: 10.1093/bioinformatics/btu031
Kallal, R. J., Kulkarni, S. S., Dimitrov, D., Benavides, L. R., Arnedo, M. A., Giribet, G., & Hormiga, G. (2020). Converging on the orb: denser taxon sampling elucidates spider phylogeny and new analytical methods support repeated evolution of the orb web. Cladistics , 1–19. doi: 10.1111/cla.12439
Kanehisa, M., & Goto, S. (2000). KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research , 28 (1), 27–30.
Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability.Molecular Biology and Evolution , 30 (4), 772–780. doi: 10.1093/molbev/mst010
Kriventseva, E. V., Kuznetsov, D., Tegenfeldt, F., Manni, M., Dias, R., Simão, F. A., & Zdobnov, E. M. (2019). OrthoDB v10: Sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. Nucleic Acids Research , 47 (D1), D807–D811. doi: 10.1093/nar/gky1053
Kumar, S., Stecher, G., Peterson, D., & Tamura, K. (2012). MEGA-CC: Computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics ,28 (20), 2685–2686. doi: 10.1093/bioinformatics/bts507
Lee, E., Helt, G. A., Reese, J. T., Munoz-Torres, M. C., Childers, C. P., Buels, R. M., … Lewis, S. E. (2013). Web Apollo: A web-based genomic annotation editing platform. Genome Biology ,14 (8). doi: 10.1186/gb-2013-14-8-r93
Letunic, I., & Bork, P. (2007). Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation.Bioinformatics , 23 (1), 127–128. doi: 10.1093/bioinformatics/btl529
Macías-Hernández, N., López, S. de la C., Roca-Cusachs, M., Oromí, P., & Arnedo, M. A. (2016). A geographical distribution database of the genus Dysdera in the Canary Islands (Araneae, Dysderidae).ZooKeys , 2016 (625), 11–23. doi: 10.3897/zookeys.625.9847
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., Von Haeseler, A., … Teeling, E. (2020). IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.Molecular Biology and Evolution , 37 (5), 1530–1534. doi: 10.1093/molbev/msaa015
Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E. L. L., … Bateman, A. (2021). Pfam: The protein families database in 2021. Nucleic Acids Research , 49 (D1), D412–D419. doi: 10.1093/nar/gkaa913
Ni, L. (2021). The Structure and Function of Ionotropic Receptors inDrosophila . Frontiers in Molecular Neuroscience ,13 (February), 1–11. doi: 10.3389/fnmol.2020.638839
Pekár, S., Líznarová, E., & Řezáč, M. (2016). Suitability of woodlice prey for generalist and specialist spider predators: A comparative study. Ecological Entomology , 41 (2), 123–130. doi: 10.1111/een.12285
Pollard, M. O., Gurdasani, D., Mentzer, A. J., Porter, T., & Sandhu, M. S. (2018). Long reads: their purpose and place. Human Molecular Genetics , 27 (R2), R234–R241. doi: 10.1093/hmg/ddy177
Putnam, N. H., Connell, B. O., Stites, J. C., Rice, B. J., Hartley, P. D., Sugnet, C. W., … Rokhsar, D. S. (2016). Chromosome-scale shotgun assembly using an in vitro method for long-range linkage arXiv : 1502 . 05331v1 [ q-bio . GN ] 18 Feb 2015. Genome Research , 26 , 342–350. doi: 10.1101/gr.193474.115.Freely
Řezáč, M., Pekár, S., & Lubin, Y. (2008). How oniscophagous spiders overcome woodlouse armour. Journal of Zoology , 275 (1), 64–71. doi: 10.1111/j.1469-7998.2007.00408.x
Řezáč, Milan, & Pekár, S. (2007). Evidence for woodlice-specialization in Dysdera spiders: Behavioural versus developmental approaches.Physiological Entomology , 32 (4), 367–371. doi: 10.1111/j.1365-3032.2007.00588.x
Řezáč, Milan, Pekár, S., Arnedo, M., Macías-Hernández, N., & Řezáčová, V. (2021). Evolutionary insights into the eco-phenotypic diversification of Dysdera spiders in the Canary Islands. Organisms Diversity and Evolution , 79–92. doi: 10.1007/s13127-020-00473-w
Robertson, H. M., Baits, R. L., Walden, K. K. O., Wada-Katsumata, A., & Schal, C. (2018). Enormous expansion of the chemosensory gene repertoire in the omnivorous German cockroach Blattella germanica .Journal of Experimental Zoology Part B: Molecular and Developmental Evolution , 330 (5), 265–278. doi: 10.1002/jez.b.22797
Saha, S. (2019). Long range sequencing and validation of insect genome assemblies. In Humana Press (Ed.), Methods in Molecular Biology(Vol. 1858). Springer New York. doi: 10.1007/978-1-4939-8775-7_4
Sánchez-Herrero, J. F., Frías-López, C., Escuer, P., Hinojosa-Alvarez, S., Arnedo, M. A., Sánchez-Gracia, A., & Rozas, J. (2019). The draft genome sequence of the spider Dysdera silvatica (Araneae, Dysderidae): A valuable resource for functional and evolutionary genomic studies in chelicerates. GigaScience , 8 (8), 1–9. doi: 10.1093/gigascience/giz099
Sanggaard, K. W., Bechsgaard, J. S., Fang, X., Duan, J., Dyrlund, T. F., Gupta, V., … Wang, J. (2014). Spider genomes provide insight into composition and evolution of venom and silk. Nature Communications , 5 (May). doi: 10.1038/ncomms4765
Schwager, E. E., Sharma, P. P., Clarke, T., Leite, D. J., Wierschin, T., Pechmann, M., … McGregor, A. P. (2017). The house spider genome reveals an ancient whole-genome duplication during arachnid evolution.BMC Biology , 15 (1), 1–27. doi: 10.1186/s12915-017-0399-x
Seppey, M., Manni, M., & Zdobnov, E. M. (2019). BUSCO: Assessing Genome Assembly and Annotation Completeness BT - Gene Prediction: Methods and Protocols . Retrieved from https://doi.org/10.1007/978-1-4939-9173-0_14
Sharma, P. P., Kaluziak, S. T., Pérez-Porro, A. R., González, V. L., Hormiga, G., Wheeler, W. C., & Giribet, G. (2014). Phylogenomic interrogation of arachnida reveals systemic conflicts in phylogenetic signal. Molecular Biology and Evolution , 31 (11), 2963–2984. doi: 10.1093/molbev/msu235
Sheffer, M. M., Hoppe, A., Krehenwinkel, H., Uhl, G., Kuss, A. W., Jensen, L., … Prost, S. (2021). Chromosome-level reference genome of the European wasp spider Argiope bruennichi : A resource for studies on range expansion and evolutionary adaptation.GigaScience , 10 (1), 1–12. doi: 10.1093/gigascience/giaa148
Smit AF, H. R. (n.d.-a). RepeatMasker-4.0 . Retrieved from http://www.repeatmasker.org
Smit AF, H. R. (n.d.-b). RepeatModeler-1.0 . Retrieved from http://www.repeatmasker.org
Stanke, M., Diekhans, M., Baertsch, R., & Haussler, D. (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics , 24 (5), 637–644. doi: 10.1093/bioinformatics/btn013
Stanke, M., Schöffmann, O., Morgenstern, B., & Waack, S. (2006). Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics , 7 , 1–11. doi: 10.1186/1471-2105-7-62
Thomas, G. W. C., Dohmen, E., Hughes, D. S. T., Murali, S. C., Poelchau, M., Glastad, K., … Richards, S. (2020). Gene Content Evolution in the Arthropods. Genome Biology , 21 (15), 1–14. doi: 10.1186/s13059-019-1925-7
Toft, S., & Macías-Hernández, N. (2017). Metabolic adaptations for isopod specialization in three species of Dysdera spiders from the Canary Islands. Physiological Entomology , 42 (2), 191–198. doi: 10.1111/phen.12192
Ullmann, A. J., Lima, C. M. R., Guerrero, F. D., Piesman, J., & Black IV, W. C. (2005). Genome size and organization in the blacklegged tick,Ixodes scapularis and the Southern cattle tick, Boophilus microplus. Insect Molecular Biology , 14 (2), 217–222. doi: 10.1111/j.1365-2583.2005.00551.x
Vieira, F. G., Sánchez-Gracia, A., & Rozas, J. (2007). Comparative genomic analysis of the odorant-binding protein family in 12Drosophila genomes: purifying selection and birth-and-death evolution. Genome Biology , 8 (11), R235. doi: 10.1186/gb-2007-8-11-r235
Vizueta, J., Escuer, P., Frıas-Lopez, C., Guirao-Rico, S., Hering, L., Mayer, G., … Sanchez-Gracia, A. (2020). Evolutionary history of major chemosensory gene families across panarthropoda. Molecular Biology and Evolution , 37 (12), 3601–3615. doi: 10.1093/molbev/msaa197
Vizueta, J., Escuer, P., Sánchez-Gracia, A., & Rozas, J. (2020). Genome mining and sequence analysis of chemosensory soluble proteins in arthropods. In Methods in Enzymology (1st ed., Vol. 642). Elsevier Inc. doi: 10.1016/bs.mie.2020.05.015
Vizueta, J., Frías-López, C., Macías-Hernández, N., Arnedo, M. A., Sánchez-Gracia, A., & Rozas, J. (2017). Evolution of chemosensory gene families in arthropods: Insight from the first inclusive comparative transcriptome analysis across spider appendages. Genome Biology and Evolution , 9 (1), 178–196. doi: 10.1093/gbe/evw296
Vizueta, J., Macías-Hernández, N., Arnedo, M. A., Rozas, J., & Sánchez-Gracia, A. (2019). Chance and predictability in evolution: The genomic basis of convergent dietary specializations in an adaptive radiation. Molecular Ecology , 28 (17), 4028–4045. doi: 10.1111/mec.15199
Vizueta, J., Rozas, J., & Sánchez-Gracia, A. (2018). Comparative genomics reveals thousands of novel chemosensory genes and massive changes in chemoreceptor repertories across chelicerates. Genome Biology and Evolution , 10 (5), 1221–1236. doi: 10.1093/gbe/evy081
Vizueta, J., Sánchez-Gracia, A., & Rozas, J. (2020). bitacora: A comprehensive tool for the identification and annotation of gene families in genome assemblies. Molecular Ecology Resources ,20 (5), 1445–1452. doi: 10.1111/1755-0998.13202
Wheeler, W. C., Coddington, J. A., Crowley, L. M., Dimitrov, D., Goloboff, P. A., Griswold, C. E., … Zhang, J. (2017). The spider tree of life: phylogeny of Araneae based on target-gene analyses from an extensive taxon sampling. Cladistics , 33 (6), 574–616. doi: 10.1111/cla.12182
World Spider Catalog. (2021). World Spider Catalog. doi: 11 June 2015
Zhang, Z. Q. (2011). Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa ,3148 , 165–191. doi: 10.11646/zootaxa.3148.1.2
Zhang, Z. Q. (2013). Phylum arthropoda. Zootaxa , 3703 (1), 17–26. doi: 10.11646/zootaxa.3703.1.6